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Article

Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

by
Zhi-Qiong Mo
1,2,†,
Jie Wang
1,2,3,†,
Michael Möller
4,
Jun-Bo Yang
3 and
Lian-Ming Gao
1,5,*
1
CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
2
University of Chinese Academy of Sciences, Beijing 100049, China
3
Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
4
Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
5
Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang 674100, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2023, 24(17), 13216; https://doi.org/10.3390/ijms241713216
Submission received: 28 July 2023 / Revised: 20 August 2023 / Accepted: 22 August 2023 / Published: 25 August 2023
(This article belongs to the Special Issue Plant Phylogenomics and Genetic Diversity)
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Abstract

:
Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study.

1. Introduction

Accurate species identification is key to conservation and biological research, such as the inference of phylogenetic relationships and unravelling the biogeographic history of taxa. The availability and affordability of next-generation sequencing (NGS) technologies have greatly expanded the use of genomic data. For instance, the next-generation barcodes (the completed plastome and the nuclear ribosomal DNA cistron (nrDNA), consisting of the 18S small-subunit (SSU) of the ribosomal RNA (rRNA) gene, the internal transcribed spacer 1 (ITS1), the 5.8S rRNA gene, the internal transcribed spacer 2 (ITS2), and the 26S large-subunit (LSU) rRNA gene) easily assembled from genome skimming data, have shown a great promise for reliably distinguishing closely related species [1,2,3,4,5]. In addition, the plastid genome contains a large number of evolutionarily informative variations, which are widely used for phylogenetic reconstruction at deep to shallow levels in land plants [6,7,8,9,10]. Crucially, the inclusion of multiple individuals from different populations across the entire distribution range of all species is needed to ensure the accurate species delimitation and correct inference and interpretation subsequently of their phylogenetic relationships [11,12]. However, very few studies hitherto have used multiple individuals per species with genomic data or included all species within a given genus.
Plant material for most endangered, rare and narrowly distributed species are difficult to gather in the field, whereas botanical gardens and arboretums typically hold a wide diversity of well-documented living plant collections, which are important resources for the purpose of scientific research, conservation, display and education [13]. However, the morphological characters of plants growing in ex situ conditions may change, which may lead to misidentification if the plants lack complete or clear origin information. In addition, mislabeling and misidentification before and after introduction into botanical gardens may also be a major cause of species misidentification. Misidentification of species collected from botanical gardens were reported in recent studies [11,13,14], which caused the incorrect inference of phylogenetic relationships and biogeographic history inferences. For instance, Le et al. [13] found that 110 out of 669 palm samples (16.4%) collected from botanical gardens were misidentified, which can also be a problem for reintroduction efforts. De Luca et al. [15] confirmed some Erythrina plants introduced or now cultivated in the ancient gardens of Naples were misidentified. Therefore, misidentification may spread misleading knowledge and result in the failure of species conservation, whereas verifying the identification of cultivated plant samples using DNA barcodes possibly can avoid misidentification leading to mistakes in biological studies or in conservation-linked reintroduction programs [13].
Torreya is a small coniferous genus in the family Taxaceae with an East Asia (EA)–North America (NA) disjunctive distribution [16,17], comprising six to eight species depending on the taxonomy classification followed [18,19,20,21]. Two species, Torreya taxifolia Arn. and T. californica Torr., occur in West and Southeast North America, respectively. Torreya taxifolia is restricted to a few ravines along the Appalachicola River in northern Florida and southern Georgia, and it is currently listed as critically endangered on The IUCN Red List of Threatened Species [22]. Torreya californica is endemic to the coastal ranges and Sierra Nevada of California and listed as vulnerable [16,23]. The other species are distributed in East Asia, they usually occur in the understory of broad-leaved or mixed broad-leaved-conifer forest [18]. Torreya nucifera Siebold and Zucc. is confined to Japan and Korea, and the remaining taxa (T. grandis Fortune ex Lindl., T. jackii Chun, T. fargesii Franch., T. yunnanensis W.C. Cheng and L.K. Fu, and T. parvifolia T.P. Yi, Lin Yang and T.L. Long) are native to China [18,20,21,24]. Of these, T. fargesii is listed as vulnerable [25], and T. jackii [26] and T. yunnanensis are listed as endangered species [27]. The taxonomy of Torreya is primarily based on morphological characters and geographical distribution of individual taxa, and the species delimitation is controversial [18,20,24]. For instance, Farjon [18] recognized six species and two varieties in Torreya. In this classification, T. parvifolia, confined to SW Sichuan province, was merged into T. grandis occurring in East China, and T. yunnanensis, native to Northwest Yunnan province, was treated as a variety of T. fargesii, distributed in Central China. On the other hand, Yang et al. [20] treated the two taxa, T. parvifolia and T. yunnanensis, as distinct species. Also, T. grandis var. jiulongshanensis Zhi Y. Li, Z.C. Tang and N. Kang, endemic to South Zhejiang of East China, was recently treated as an independent species [28]. This species was later shown to be a likely hybrid origin between two sympatric species, T. jackii and T. grandis, with the latter being the paternal parent [29]. Therefore, currently, nine species are recognized in Torreya, though more evidence to confirm their genetic species boundaries are needed, such as the entire plastome as next-generation barcode, which has shown great ability for distinguishing species in Taxaceae [11,12].
The monophyly of Torreya is supported by both morphology and molecular data [30,31]. However, published phylogenetic species relationships within the genus are conflicting, sometimes even when based on the same genomic markers [14,16,29,31,32,33]. For instance, the phylogenetic analysis of seven species based on nuclear RAD-seq genomic data resolved two monophyletic clades, the NA species clade and the EA species clade, the latter being: (T. fargesii + T. yunnanense) (T. jackii (T. grandis + T. nucifera)) with highly supported branches [14]. A plastome phylogeny showed a discordant phylogenetic position of T. jackii, which shifted to a position as sister to the rest of all other species [14]. However, also based on the complete plastome, the interspecific relationships differed from the above study in which T. jackii was also recovered as the earliest divergent species, but followed by T. taxifolia, rather than a sister clade consisting of NA species clade and other EA species clade [30,31,34,35]; other relationships saw T. californica as sister to T. grandis [30,31,34,35], and T. yunnanense was resolved as sister to a clade of T. parvifolia (T. fargesii + T. nucifera), and these two clades form a sister relationship [30,34]. These species formed a clade but had inconsistent relationships in Miao et al. [35] and Ji et al. [31]. Here, T. nucifera was sister to T. californica + T. grandis, while T. yunnanense clustered with T. parvifolia to form a sister relationship with T. fargesii + T. nucifera in Miao et al. [35]. Torreya nucifera was sister to a clade of T. yunnanensis (T. californica + T. grandis), and then formed a sister relationship with T. parvifolia + T. fargesii in Ji et al. [31].
As several species in Torreya are listed as endangered species with small distribution ranges, the plant material of some species used for previous molecular phylogenies came from cultivated plants in botanical gardens/arboretums, and only a single accession for each species was sampled in previous studies [30,31,33,34,35]. The misidentification of this cultivated plant material may have led to the discordances between the previous studies. For instance, the samples of T. californica and T. nucifera (GenBank ID: MK249062 and MK249060, respectively), collected from botanical gardens and used in Zhang et al. [30], were suspected to be misidentified based on their phylogenetic placement and/or examination of their photographs [14]. In any case, thus far, the proportion of cultivated plant accessions of Torreya misidentified in previous studies is unknown.
The phylogenetic discordance between nuclear and organelle, and between organelles (plastome and mitochondrion) may result from hybridization and/or introgression, and plastome capture events, which are due to the different inheritance patterns of the genomes [36]. The plastid genome is paternal inheritance in some Taxaceae [37,38], while the inheritance of the mitochondrial genome can be paternal or maternal in conifers and can include recombination [37,39], though it is partly maternal in Taxaceae [40], or seemingly maternal for both mitochondria and plastids in Torreya [41]. Comparing the concordance and/or discordance of nuclear and organelle phylogenies may aid to explore the evolutionary history and the inheritance model of the organelle within Torreya.
In this study, we acquired the next-generation barcode (complete plastid genome and nrDNA cistron) and mitochondrial genes for all Torreya species currently accepted [18,20,28], except for the recently described species T. dapanshanica X.F. Jin, Y.F. Lu and Zi L. Chen [42]. We included multiple individuals per species. We also added all available published complete plastomes, nrDNA cistrons and mitochondrial genes from the same individuals for analysis. A Skmer [43] analysis, which can use the entire nuclear reads generated in a genome skim as the identifier of a species [44] rather than just the highly repetitive nrDNA sequences, was also used for Torreya species identification. Explicitly, we aimed to: (1) evaluate the efficiency of the next-generation barcode and nuclear genome information obtained by Skmer for species delineation of species within Torreya; (2) determine the proportion of misidentification of cultivated plants from botanical gardens; (3) infer the phylogenetic species’ relationships within Torreya.

2. Results

2.1. Plastomes, Mitochondrial Genes and nrDNA Cistrons of Torreya

Complete circular plastid genomes of the 19 newly sequenced Torreya individuals were assembled with high quality, with an average sequencing coverage of 223 to 1144 × (Table 1). The plastomes of all Torreya accessions had a length ranging from 136,693 bp to 137,412 bp. Their average GC content was similar (35.4–35.5%; Table 1). The plastomes consisted of 118 unique genes, comprising 83 protein-coding genes, 31 tRNA genes and four rRNA genes. Of these, three genes, trnI-CAU, trnN-GUU and trnQ-UUG, each had two copies. Similar to the published plastomes of Torreya (e.g., T. parvifolia NC_043866, T. taxifolia MK249063 and T. jackii KX902234), an inverted repeat region was not found in the newly assembled plastomes.
A total of 26 mitochondrial genes and the complete nrDNA cistron of 26 Torreya samples and two species of Amentotaxus were assembled and extracted. Of these, the mitochondrial genes of one Torryeya sample (SRR10768423) had many missing data and was removed from the mitochondrial phylogenetic analyses.
The length of the three unfiltered genomic sequence matrices, CP, MT and nrDNA, was 145,775 bp, 21,493 bp, and 6137 bp, respectively. For the samples of Torreya, Matrix CP had 2561 variable sites (1.82%) and 2063 parsimony informative (PI) sites (1.47%). The nrDNA cistron matrix had 52 variable (0.85%) and 44 PI (0.72%) sites, among which ITS1 accounted for the largest proportion (39 variable and 34 PI sites), followed by ITS2 (6 sites for both), 28S (5 variable and 3 PI sites), and 5.8S (2 variable and 1 PI sites), while 18S showed no variation. Matrix MT had the lowest proportions of both variable (0.07%; 14 total) and PI (0.03%; 7 total) sites among the three matrices. The proportion of variable and PI sites in the filtered matrices changed only slightly, and the filtered Matrix MT still contained the lowest values (Table 2).

2.2. Phylogenetic Analyses—Species Delineation and Sample Identities

The unfiltered and filtered matrices of CP, nrDNA and MT yielded identical topologies, but the filtered matrices received relatively higher support values. Here, only the results from the filtered matrices (CP-gb, nrDNA-gb and MT-gb) are reported. The plastid phylogenetic tree showed that all taxon clades had high support values (BS ≥ 95%; PP = 1) (Figure 1A). Five out of the nine sampled species formed species-specific clades, except T. nucifera, T. californica, T. jiulongshanensis, and T. yunnanensis. The samples of T. nucifera formed a grade of two clades as sister to T. grandis. The three accessions of T. californica fell distantly in different clades, To39 as sister to the T. taxifolia clade, To38 in the larger T. nucifera clade, and MK249062 as sister to T. jiulongshanensis MN244714 in the T. grandis clade. The second T. jiulongshanensis sample, NC_050372, was placed in the T. jackii clade. One sample of T. yunnanensis, NC_056892, fell in the smaller T. nucifera clade (Figure 1A).
In the nrDNA-gb phylogenetic tree, five well to highly supported clades were received (BS ≥ 83%; PP ≥ 0.98) (Figure 1B), with four being species-specific, T. grandis, T. jackii, T. nucifera, and T. taxifolia. Additionally, here, the two T. californica samples fell in different clades, To38 in the T. nucifera clade, and To39 as sister to the T. taxifolia clade. Samples of three species, T. fargesii, T. parvifolia, and T. yunnanensis, fell in a polytomy. The single accession of T. jiulongshanensis, SRR10758782 (MN244714 in the plastome tree), fell into the clade of T. grandis (Figure 1B).
The mitochondrial phylogeny, MT-gb, showed low phylogenetic resolution (Figure S2). However, moderately to highly supported (BS ≥ 41%; PP ≥ 0.98) species-specific clades were found for T. grandis, T. jackii, T. nucifera, and T. taxifolia, as in the nrDNA-gb tree. The positions of the two T. californica samples were identical to those in the cpDNA-gb and nrDNA-gb trees. The single accession of T. jiulongshanensis, SRR10758782 (MN244714 in the plastome tree), fell into the T. jackii clade (Figure S2), different from its position in the plastome and nrDNA cistron trees where it was in the T. grandis clade (Figure 1). In the plastid tree, the other T. jiulongshanensis sample, NC_050372, was associated with the T. jackii clade. The phylogenetic relationships of the samples of T. fargesii, T. parvifolia, and T. yunnanensis were not well resolved (Figure S2).
The Skmer analysis showed that all sampled Torreya species, except T. californica, with multiple accessions per species (i.e., excluding T. jiulongshanensis with one sample), were resolved in species-specific clades (Figure 2). These were basically the same grouping based on plastome and nrDNA cistron data (Figure 1). Although, the T. californica sample To38 was resolved with T. californica sample To39 and T. taxifolia clade, which was different in both the CP and nrDNA cistron trees.

2.3. Discordance between Plastid, nrDNA Cistron, and Mitochondrial Phylogenies

To compare phylogenetic species relationships inferred from different genomic data, one sample of each species that was correctly identified, based on next-generation DNA barcoding, was used for phylogenetic analysis. The interspecific relationships within Torreya were fully resolved with maximum support values using the complete plastome data (BS = 100%, PP = 1; Figure 3A). Here, T. jackii formed the earliest diverging species, and the clade of NA species, T. taxifolia and T. californica, was sister to the remaining species from East Asia. These formed two clades, i.e., T. yunnanensis (T. parvifolia + T. fargesii), and T. nucifera + T. grandis.
The nrDNA cistron phylogenetic tree showed similar species relationships compared to the plastome tree (Figure 3B). However, here T. jackii was resolved as sister of T. grandis, although not with high branch support all along the branches to the backbone (BS ≤ 73%; PP ≤ 0.98). The phylogenetic tree based on mitochondrial genes had low phylogenetic resolution and, in general, low branch support values (BS ≤ 72%; PP ≤ 1.0) (Figure 3C). Torreya taxifolia was sister to T. californica with low support value (BS = 40%), and T. fargesii, T. yunnanensis and T. parvifolia formed a polytomy (BS = 72%). Different from the phylogenies of plastome and nrDNA cistron sequences, the relationships between these two clades and the other three species, T. grandis, T. jackii and T. nucifera, were unresolved.

3. Discussion

3.1. Species Delimitation and Correction of Misidentified Accessions

The plastome was proposed as a super-barcode to distinguish species in Taxaceae with high species discrimination ability [11,12]. Recently, an alternative approach, Skmer, was proposed for sample identification, using unassembled genome skims, which can effectively improve the phylogenetic signal and identification resolution [50,51]. In the present study, all the nine Torreya species recognized in past treatments with multiple samples were analyzed with the next-generation DNA barcode and Skmer. All the 21 wild collected samples of the EA species formed species-specific clades, except T. jiulongshanensis, whose two sampled individuals fell into the T. jackii and the T. grandis clades, respectively (Figure 1), and was regarded a natural hybrid between T. jackii and T. grandis based on morphology and molecular markers [29] (see Section 3.2. below).
For the 17 accessions from botanical gardens/arboretums, 12 accessions grouped into their corresponding species clades and the one accession of T. californica (To39) formed a distinct lineage sister to T. taxifolia, while the remaining four accessions fell in other species clades in the plastome tree, indicating possible misidentification of these samples. Of these four, one accession (NC_056892) of ‘T. yunnanensis’ fell into the clade of T. nucifera, but not in the clade of T. yunnanensis including five accessions from wild populations. This accession was from an introduced plant in the Kunming Botanic Garden of the Chinese Academy of Sciences, which was confirmed to represent T. nucifera after checking this living collection. The same was the case for accession MK249060 of ‘T. nucifera’ from Lushan Botanic Garden (Jiangxi, China), which fell in the clade of T. fargesii, and was confirmed to represent a misidentification by examining a photo of the voucher for this accession [14]. Of the other two accessions (MK249062 and To38) identified as T. californica that fell in the T. grandis and T. nucifera clades, respectively, in the plastome tree, accession MK249062, used in Zhang et al. [30], was regarded misidentified and identified as T. grandis based on the result in our study (Figure 1 and Figure S1) as well as in Zhou et al. [14]. The accession To38, which was also sampled and sequenced in Zhou et al. [14] as Xianglab209, however, was not included for analysis in Zhou et al. [14], due to a high amount of missing data. In the present study, our resampled and sequenced accession To38/Xianglab209 had no missing data and fell in the clade of T. nucifera in the plastome, nrDNA cistron and MT trees, but it was resolved as a sister to clade of T. californica (To39) and T. taxifolia in the Skmer analysis. This indicates that it may be misidentified and, likely, its hybrid origin is between T. nucifera and T. californica. Therefore, accession To39 with a consistent placement in the phylogenies is assumed to represent a T. californica accession.
The accessions of T. nucifera formed two clades with high support in the plastome tree, indicating a possible cryptic species. However, the accessions of this species (To35, To36, To37, and SRR10768423) were grouped into a clade in the nrDNA cistron tree without any intraspecific genetic variation (Figure 1B). Torreya nucifera is endemic to Japan and South Korea, and the plastome is inherited maternally through seed. Therefore, plastid genome capture from T. grandis during an ancient secondary contact might be more feasible than a new cryptic lineage derived from T. nucifera for the clade sister to T. grandis in the plastome tree. Further detailed molecular and morphological studies are needed to elucidate this issue.
If the misidentified accessions are corrected and disregarding the putative hybrid T. jiulongshanensis and smaller T. nucifera clade, then all eight recognized species in Torreya sampled here were resolved as “good” species and were successfully discriminated based on the super-barcode of the complete plastid genome, as well as the Skmer analysis (excluding To38) with unassembled nuclear reads. It was notable that three species, T. yunnanensis, T. fargesii and T. parvifolia, were closely related and formed a single clade in nrDNA cistron and mitochondrial phylogenies without much variation (Figure 3), simply due to a shortage of variable sites, perhaps due to their short divergent time. Their relatively short branch lengths in the plastome phylogeny may further support their possibly recent allopatric divergence. However, the plastome tree and Skmer analyses allows the unambiguous delineation. Thus, it may be more appropriate to treat them at a subspecies level because they have distinct distribution range and a similar morphology, with only minor differences in seed traits [18,24]. Historically, Kang and Tang [52] treated T. yunnanensis as a variety of T. fargesii, and Farjon [18] accepted this taxonomic treatment. While Farjon [18] merged T. parvifolia into T. grandis, this was not supported in our study. On the other hand, Yi et al. [53] identified T. parvifolia as closely related to T. yunnanensis, and treated it as an independent species. Based on our results, we support the treatment of both T. yunnanensis and T. parvifolia as two varieties of T. fargesii, as T. fargesii var. yunnanensis and T. fargesii var. parvifolia, respectively.
Collectively, the proportion of misidentification of cultivated plants of Torreya held in botanical gardens was relatively high, being 23.5% (4 out of 17 accessions). Since the four accessions represented three species, the misidentification at species level was much higher with 37.5% (3 out of 8). In Zhang et al. [30], two of the seven sampled species were misidentified, which directly affected their inference of phylogenetic relationships and biogeographic history. In addition, species misidentification may also lead to mistakes in conservation-linked reintroduction programs, which reduces the scientific value of botanical garden/arboretum collections. Therefore, more caution should be taken when using cultivated plants from botanic gardens/arboretums for biological study, and there is a need for the verification of their species identification. In previous molecular studies [30,34,35], sequences were downloaded from GenBank or obtained from cultivated plants directly without concerns of species identification, which may have affected their phylogenetic inferences. The use of multiple samples per species in this respect cannot be overemphasized as only this allowed an independent check for correct species identifications [11]. At present, species identification of cultivated plants is of little concern, but fortunately some projects aim at comprehensive sequencing were conducted, such as sequencing for an entire botanical garden [54], which may provide a large amount of fundamental data for assessing identification issues of cultivated plants.

3.2. Hybrid Origin of T. jiulongshanensis

In this study, the non-monophyly of T. jiulongshanensis, already mentioned above, involved two sampled accessions falling into two clades representing T. grandis and T. jackii in the complete plastome tree (Figure 1). Torreya jiulongshanensis is endemic to South Zhejiang of East China and occurs within the sympatric region of T. jackii and T. grandis. Its morphological characters, especially leaf length and seed size, are intermediate between these two species [29]. Based on nuclear internal transcribed spacer (ITS) and plastid rbcL and rpl16 sequences, Kou et al. [29] suggested T. jiulongshanensis to be a natural hybrid between T. grandis and T. jackii with the latter being the maternal parent due to the shared plastid haplotype with T. jiulongshanensis. It needs to be noted that the cytoplasm, i.e., plastome and mitochondria, in Torreya are apparently maternally inherited [41]. Given this, the fact that the two T. jiulongshanensis accessions fell with both species strongly suggests repeated and reciprocal hybridizations occurred. An alternative explanation may be leakage of the male cytoplasm, as observed for angiosperms and gymnosperms such as Pinus L. [37,55]. This might also explain the placement of one accession of T. jiulongshanensis (SRR10758782, the same accession of MN244714 in the plastome tree) with T. grandis in the plastome, nrDNA cistron trees, and Skmer analysis (Figure 1 and Figure 2), and grouping with T. jackii in the mitochondrial phylogeny (Figure S2). Overall, we can conclude that T. jiulongshanensis is a natural hybrid, in fact, more precisely, nothospecies T. × jiulongshanensis, between T. jackii and T. grandis with repeated bidirectional hybridization. To elucidate the exact cytoplasm inheritance patterns in Torreya would require further detailed studies.

3.3. Phylogenetic Relationships and Conflicts among the Three Genomic Phylogenies

Hybridization/introgressions, polyploidizations, and incomplete lineage sorting (ILS) may contribute to phylogenetic conflicts between nuclear and organelle phylogenies [36]. Discordances of the interspecific relationships within Torreya were revealed among the different genomic data. This was especially the case between the plastid topology on the one hand and the nuclear and mitochondrial topologies on the other (Figure 3). The unresolved relationship between the two species, T. grandis and T. nucifera, in the mitochondrial phylogenetic tree, as opposed to a sister relationship in the plastome tree, is likely an artefact of the low diversity of the MT sequences as shown in the low branch support. This is also reflected in the monophyly of the two NA species, T. californica and T. taxifolia, in the mitochondrial phylogenetic tree with the branch support of only 40%, compared with 93% and 100% in the nrDNA cistron and plastome trees, respectively. The main conflict between the phylogenies was in the placement of T. jackii as the first diverging lineage in the plastid tree, and as a member in a clade with T. grandis and T. nucifera in the nrDNA cistron tree. This was also found in previous studies [14,29,32]. Zhou et al. [14] suggested that the conflict was difficult to explain and that it could be the result of differential lineage sorting of a dimorphic ancestral chloroplast genome among species and clades of Torreya, or as the result of chloroplast capture by T. jackii from Amentotaxus. The latter, however, is very unlikely since it would require a recent hybridization event between very distant lineages. A more likely scenario is an introgressive hybridization event between T. jackii and T. grandis, with T. jackii being the maternal parent.

4. Materials and Methods

4.1. Sample Collection, DNA Extraction and Genome Skimming Sequencing

Our samples included 38 accessions of Torreya with multiple samples (2 to 6) of nine species following the most recent taxonomic classifications [18,20,28] (Table 1) that were sampled across their distribution ranges (Figure S1). For 19 of these, fresh leaves of either cultivated or wild field-collected individuals were sampled and dried immediately in silica-gel for DNA extraction. Voucher specimens were deposited at the Herbarium of Kunming Institute of Botany (KUN), Chinese Academy of Sciences. For the other 19 samples, the complete plastomes were downloaded from GenBank as available on 20 February 2023. The corresponding raw sequencing data (only available for seven accessions) were downloaded from the NCBI Sequence Read Archive (SRA) for nrDNA and mitochondrial genome assembly. Of these 38 samples, 21 came from the field and 17 came from arboretums/botanical gardens. Amentotaxus yunnanensis H.L. Li and A. formosana H.L. Li were selected as outgroups for data analyses (Table 1).
Total genomic DNA was extracted from silica-gel dried leaves using a modified CTAB method [56], and was quantified and sheared to a mean insert size of 500 bp for Illumina library construction with a TruSeq DNA Sample Prep Kit following the manufacturer’s instructions (NEBNext® Ultra IITMDNA Library Prep Kit for Illumina®). The libraries were sequenced for each sample on an Illumina HiSeq X Ten platform (Illumina, San Diego, CA, USA) with 150 bp paired-end reads at BGI Wuhan, China. Adaptors and low-quality reads were filtered using fastp v0.21.0 [57] with default parameters. Improvement in read quality was checked using FastQC v0.11.5 (available from http://www.bioinformatics.babraham.ac.uk/projects/fastqc (accessed on 25 June 2018)).

4.2. Assembly and Annotation

The plastomes of the 19 newly sampled individuals were assembled from clean reads using the GetOrganelle toolkit [58]. The mitochondrial genomes and nrDNA cistrons of these newly sequenced individuals and the SRA data file reads were also assembled by GetOrganelle. In this pipeline, target-associated reads were recruited by Bowtie2 v2.3.4 [59], extracted from total genomic reads, and subsequently de novo assembled by SPAdes v3.15 [60]. Then, the slimmed assembly graph (FASTG) of each sample was visualized by Bandage [61] and the complete plastome and nrDNA cistron sequences were exported. The extracted plastome sequences of all newly sampled individuals, collineating with the reference (Torreya grandis NC_034806), were retained for subsequent analysis. Plastid genes were annotated using PGA [62] with the published plastome of T. grandis (NC_034806) as the reference and manually adjusted in Geneious v9.0.2 [63]. Transfer RNAs (tRNAs) were confirmed by tRNAscan-SE v2.0.3 [64]. The nrDNA cistrons were annotated using Geneious with Chamaecyparis formosensis (LC518080) as the reference. To obtain mitochondrial genes, the newly assembled mitochondrial genome scaffolds were annotated with the mitochondrial genome of Taxus cuspidata (MN593023) as the reference. The mitochondrial genes were then extracted from the annotated scaffolds using Geneious.

4.3. Phylogenetic Analyses

The complete plastome, mitochondrial genes and nrDNA cistron sequences of all accessions were aligned separately using MAFFT v7.407 [65], and manually adjusted where necessary in Geneious. The aligned sequences of the individual mitochondrial genes were concatenated in AMAS [66]. In order to assess the effect of alignment quality on the phylogeny, hypervariable and poorly alignable regions were filtered out in Gblocks v0.91b [67] using default parameters but with half-gap positions allowed.
We conducted phylogenetic analyses based on complete matrices and filtered matrices separately of the plastome (CP and CP-gb, respectively), mitochondrial genes (MT and MT-gb, respectively) and nrDNA cistrons (nrDNA and nrDNA-gb, respectively) with all accessions for species delineation using Maximum Likelihood (ML) and Bayesian Inference (BI) analyses. Before phylogenetic analysis of each matrix, PartitionFinder2 [68] was used to determine the best-fitting partitioning schemes and best-fitting nucleotide substitution models for each partition under the corrected Akaike information criterion (AICc). Linked-branch lengths with greedy search [69] was used for the matrices of mitochondrial genes and nrDNA cistrons and rcluster search [70] for the matrices of the whole plastome sequences. Each gene, intergenic region or intron (if any), was regarded as a predefined data block.
The best-fitting partitioning scheme and evolutionary model estimated for each subset were used for ML and BI analyses. The ML analyses were conducted using RAxML v8.2.12 [71] with the option of rapid bootstrap of 1000 replicates. The BI analyses were conducted using MrBayes v3.2.7a [72] with two independent runs each with four Markov chains. MrBayes was run for 10 million generations for the matrices of mitochondrial genes and nrDNA cistrons and 50 million generations for the matrices of the whole plastome, sampling every 1000 and 2500 generations, respectively. The first 25% of sampled trees were discarded as burn-in, and the remaining trees were used for generating the majority-rule consensus tree. The average standard deviation of split frequencies was ensured to reach a value less than 0.01, and the convergence of the MCMC chains was checked in Tracer v1.7.2 [73].
To determine the phylogenetic relationships within Torreya and obtain a species level tree, only one accession collected from the field, as far as possible, and correctly identified here for each species, excluding the hybrid Torrey jiulongshanense, was retained for these phylogenetic analyses. The partitioning scheme and nucleotide substitution model estimation, and ML and BI analyses were implemented as described above.

4.4. Skmer Analysis

In plant genome skimming data, most sequence data is from the nuclear genome. However, only ribosomal DNA sequences of the nuclear genome from the data are often used for species discrimination and plant phylogenetic studies, discarding a vast proportion of nuclear reads and only providing limited sequence information [44].
Skmer is an assembly-free method for estimating genomic distances between a query and reference genome skims, which can reflect the evolutionary divergence between two species for species identification [43]. We used Skmer v3.2.1 to analyze the unassembled nuclear reads of genome skimming data for Torreya species identification. Before Skmer analysis, reads of the organelle genome and the nrDNA cistron in the genome skimming data were mapped to their respective references constructed using mitochondrial genome of Taxus cuspidate mentioned above (MN593023), and plastid genome and nrDNA cistron sequences obtained in the present study, by Bowtie2, left unmatched reads (--un-conc-gz) as an input to Skmer. We used the workflow suggested by the authors to obtain the distance matrix for sequencing reads. Then, FastME v2.1.6.4 [74] was used to infer the backbone tree, and RAxML was used to generate the phylogenetic trees with support values.

5. Conclusions

We gathered wild and cultivated samples of Torreya with multiple accessions per species to evaluate a next-generation DNA barcode and Skmer for species delineation and sample identification, and to reconstruct interspecific phylogenetic relationships. All but one of the eight recognized species in Torreya were successfully discriminated based on super-barcode of the complete plastid genome (except T. nucifera) and the Skmer analysis (except T. californica), and T. jiulongshanensis was confirmed as a hybrid. The Skmer method uses unassembled nuclear reads from genome skims and significantly increased the discrimination rate compared to the nrDNA cistron and MT sequences, and could be proposed as a credible approach for species discrimination. We found that around a quarter of cultivated plants of Torreya were misidentified in botanical gardens/arboretums. This stresses the need for more caution when using cultivated plants and the need for careful verification of their identities. The interspecific phylogenetic relationships in Torreya were well-resolved with maximum support in the plastome phylogeny. Based on the robust phylogenetic topology, we preliminarily delineate the taxa greatly along recognized taxa from past treatments, with the exception of recognizing two varieties/subspecies in T. fargesii. This study enriches the existing genetic data of Torreya, and will provide genetic baseline data to facilitate the accurate species identification in the future and to confirm the identities of Torreya species in collections. The findings here shed light on the significance of the accurate species identification for biological studies, and also provide quantitative insights into the usage of cultivated samples for phylogenetic study.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/ijms241713216/s1.

Author Contributions

Conceptualization, L.-M.G.; formal analysis, Z.-Q.M. and J.W.; validation, Z.-Q.M.; investigation, J.W. and L.-M.G.; resources, L.-M.G. and J.-B.Y.; writing—original draft preparation, Z.-Q.M.; writing—review and editing, Z.-Q.M., M.M. and L.-M.G. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000), the Large-scale Scientific Facilities of the Chinese Academy of Sciences (2017-LSFGBOWS-02), the Key Basic Research Program of Yunnan Province, China (202101BC070003), and the International Partnership Program of Chinese Academy of Sciences (151853KYSB20190027). The APC was funded by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB31000000).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Sequence alignments and sequences of plastome, nrDNA cistron and mitochondrial gene have been deposited in Science Data Bank at: https://doi.org/10.57760/sciencedb.09201.

Acknowledgments

We are grateful to Renlin Liu, Kevin Burgess, Qiuyun (Jenny) Xiang, Jie Liu, Hongtao Li, Lina Zhang, Zhirong Zhang and Jing Yang for their help with sample collection, laboratory work and data analysis. Molecular experiments and data analysis were performed at the Laboratory of Molecular Biology and iFlora High-Performance Computing Center of Germplasm Bank of Wild Species, Kunming Institute of Botany.

Conflicts of Interest

The authors declare no conflict of interest.

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Ijms 24 13216 g001
Figure 1. Phylogenetic relationships of Torreya species constructed using RAxML based on the filtered plastid (A) and nrDNA cistron (B) matrices. ML tree is shown with Maximum Likelihood bootstrap (BS)/Bayesian Inference posterior probability (PP) values given for each taxon node. Cultivated samples of Torreya are marked with triangles.
Figure 1. Phylogenetic relationships of Torreya species constructed using RAxML based on the filtered plastid (A) and nrDNA cistron (B) matrices. ML tree is shown with Maximum Likelihood bootstrap (BS)/Bayesian Inference posterior probability (PP) values given for each taxon node. Cultivated samples of Torreya are marked with triangles.
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Figure 2. Skmer tree of Torreya species based on unassembled reads. Branches of each species are designated in different colors.
Figure 2. Skmer tree of Torreya species based on unassembled reads. Branches of each species are designated in different colors.
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Figure 3. Phylogenetic relationships of Torreya species constructed using RAxML based on the filtered plastid (A), nrDNA cistron (B), and mitochondrial (C) matrices. ML tree is shown with Maximum Likelihood bootstrap (BS)/Bayesian Inference posterior probability (PP) values given for each node. Nodes without values represent maximal support in both ML and BI methods. Nodes with “-” represent unsupported relationship in the tree. Internal branches shown in red are not recovered in the left plastid tree. The species name is followed by distribution information, with NA for North America and EA for East Asia.
Figure 3. Phylogenetic relationships of Torreya species constructed using RAxML based on the filtered plastid (A), nrDNA cistron (B), and mitochondrial (C) matrices. ML tree is shown with Maximum Likelihood bootstrap (BS)/Bayesian Inference posterior probability (PP) values given for each node. Nodes without values represent maximal support in both ML and BI methods. Nodes with “-” represent unsupported relationship in the tree. Internal branches shown in red are not recovered in the left plastid tree. The species name is followed by distribution information, with NA for North America and EA for East Asia.
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Table 1. Taxa and samples of Torreya and Amentotaxus included in the present study with information on voucher, locality, origin, and GenBank (Sequence Read Archive, SRA) accession numbers and NGS performance, and data sources.
Table 1. Taxa and samples of Torreya and Amentotaxus included in the present study with information on voucher, locality, origin, and GenBank (Sequence Read Archive, SRA) accession numbers and NGS performance, and data sources.
TaxonCorrect Scientific NameVoucherSample IDGenBank (SRA) Accession Number of PlastomeGenBank (SRA) Accession Number of nrDNA CistronLocality InformationOriginNo. of BasesNo. of ReadsPlastome Size (bp)No. of Reads Mapped to PlastomeMean Coverage of Plastome (×)Platome GC Content (%)Source
Amentotaxus formosana * -AM10OK138557 (SRR25021671)(SRR25021671)China: Taiwan, Pingtung 3,662,110,50024,414,070136,361450,08650035.8Wang et al. [11]
Amentotaxus yunnanensis GBOWS079AM21OR197346OR195109China: Yunnan, Malipo, Xiajinchang 1,927,772,70012,851,818137,609134,071146.235.8this study
Torreya californicaTorreya nuciferaXianglab209To38OR197360OR195123USA: North Carolina JC Arboretumcultivated1,980,844,20013,205,628137,215593,920645.835.4this study
Torreya californicaTorreya grandis--MK249062-UK: Edingburgh, Royal Botanic Garden Edinburghcultivated 136,693 35.4Zhang et al. [30]
Torreya californica * Xianglab276To39OR197361OR195124USA: Washington Arboretumcultivated3,243,790,20021,625,268136,957429,684468.535.4this study
Torreya fargesii Zhdq-195To03OR197348OR195111China: Gansu, Wenxian, Bikouwild4,098,586,80027,323,912137,055261,206279.235.5this study
Torreya fargesii --NC_029398-China: Hubei, Wuhang, Wuhan Botanic Gardencultivated 137,075 35.5Tao et al. [45]
Torreya fargesii * Zhdq-081To02OR197347OR195110China: Sichuan, Maoxian, Fengyiwild2,744,998,80018,299,992137,047206,326223.335.5this study
Torreya grandis LJ-10759To31OR197355OR195118China: Zhejiang, Linan, Tianmushan Nature Reservewild3,982,402,80026,549,352136,991487,543556.735.4this study
Torreya grandis 061013-8To04OR197349OR195112China: Jiangxi, Qianshan, Wuyishan Natural Reservewild2,342,818,50015,618,790136,962219,046236.135.4this study
Torreya grandis --NC_034806-China: Zhejiang, Hangzhou, Hangzhou Botanical Gardencultivated 136,949 35.4Miu et al. [46]
Torreya grandis * ZLN-2011120To29OR197354OR195117China: Fujian, Nanping, Wuyishan Natural Reservewild4,690,482,30031,269,882136,948281,539302.735.4this study
Torreya jackii GLM-07317To07OR197350OR195113China: Yunnan, Kunming, Kunming Botanical Gardencultivated2,766,930,60018,446,204136,798398,596433.635.5this study
Torreya jackii -To43OK138558 (SRR25021670)(SRR25021670)China: Jiangxi, Zixi, Matuoshanwild3,865,107,90025,767,386136,884451,82549535.5Wang et al. [11]
Torreya jackii --NC_056893-China: Yunnan, Kunming, Kunming Botanical Gardencultivated 136,924 35.5Ji et al. [31]
Torreya jackii --MK249064-China: Zhejiang, Hangzhou, Hangzhou Botanical Gardencultivated 136,728 35.5Zhang et al. [30]
Torreya jackii --KX902234-China: Zhejiang, Tonglu, Baiyunyuan Forest Parkwild 136,720 35.5Li et al. [47]
Torreya jackii * PVHJX03232To42OR197362OR195125China: Jiangxi, Zixi, Matuoshanwild3,073,291,50020,488,610136,751343,308374.335.5this study
Torreya jiulongshanensis --NC_050372-China: Zhejiang, Jingning, Xikengxia Villagewild 136,705 35.5Jiang et al. [48]
Torreya jiulongshanensis --MN244714 (SRR10758782)(SRR10758782)China: Zhejiang, Suichang, Jiulong Mountain Nature Reservewild3,842,990,16625,450,266137,320574,469755.835.4Miao et al. [35]
Torreya nucifera 19940566To35OR197357OR195120USA: Atlanda, Atlanta Botanical Gardencultivated6,329,296,22442,242,036136,944630,323685.335.5this study
Torreya nucifera 19940647To36OR197358OR195121USA: Atlanda, Atlanta Botanical Gardencultivated5,910,584,36639,445,718136,9441,051,3441144.535.5this study
Torreya nucifera --MK978775-South Korea: Pyungdae-ri, Jeju-do Islandwild 136,985 35.4Shin et al. [49]
Torreya nuciferaTorreya fargesii--MK249060-China: Jiangxi, Jiujiang, Lushan Botanical Gardencultivated 136,970 35.5Zhang et al. [30]
Torreya nucifera --MN244713 (SRR10768423)(SRR10768423)China: Jiangshu, Nanjing, Nanjing Universitycultivated3,495,500,20823,149,008136,955238,714261.535.5Miao et al. [35]
Torreya nucifera * 19980776To37OR197359OR195122USA: Atlanda, Atlanta Botanical Gardencultivated5,231,130,27034,919,542137,276247,792269.235.4this study
Torreya parvifolia 5025To44OR197363OR195126China: Sichuan, Tuowu, Wuyi Townwild7,353,802,22249,770,264137,160694,509779.735.5this study
Torreya parvifolia W24To46OR197365OR195128China: Sichuan, Tuowu, Wuyi Townwild7,520,255,40050,135,036137,183587,44663935.5this study
Torreya parvifolia --NC_043866 (SRR13235763)(SRR13235763)China: Sichuan, Liangshanwild12,258,497,81981,276,138137,106512,642561.735.5Zhang et al. [34]
Torreya parvifolia --MN244711 (SRR10769481)(SRR10769481)China: Sichuan, Butuo, Wuyi, Wandun Mountainwild4,853,642,83032,143,330136,781264,197290.535.5Miao et al. [35]
Torreya parvifolia * W21To45OR197364OR195127China: Sichuan, Tuowu, Wuyi Townwild7,492,564,20049,950,428137,198342,748374.435.5this study
Torreya taxifolia -To33NC_063708 (SRR25021669)(SRR25021669)USA: Atlanda, Atlanta Botanical Gardencultivated5,860,851,36439,120,638137,117452,291498.835.4Wang et al. [11]
Torreya taxifolia --MK249063-USA: Atlanda, Atlanta Botanical Gardencultivated 137,285 35.4Zhang et al. [30]
Torreya taxifolia * 20121421To34OR197356OR195119USA: Atlanda, Atlanta Botanical Gardencultivated5,707,656,42838,089,352136,972444,007485.535.4this study
Torreya yunnanensis GLM-07342To09OR197351OR195114China: Yunnan, Yulong, Xinzhuwild3,523,821,90023,492,146137,074506,145549.135.5this study
Torreya yunnanensis GLM-092567-1To26OR197353OR195116China: Yunnan, Weixi, Weidengwild4,241,168,70028,274,458137,122399,311430.735.5this study
Torreya yunnanensisTorreya nucifera--NC_056892-China: Yunnan, Kunming, Kunming Botanical Gardencultivated 137,412 35.4Ji et al. [31]
Torreya yunnanensis GLM-07342-1-MK249061-China: Yunnan, Yulongwild 136,844 35.5Zhang et al. [30]
Torreya yunnanensis --MN244712 (SRR10758697)(SRR10758697)China: Yunnan, Weixiwild4,151,493,13227,493,332136,807233,61325635.5Miao et al. [35]
Torreya yunnanensis * GLM-07469To25OR197352OR195115China: Yunnan, Gongshan, Bingzhongluowild4,142,196,60027,614,644137,029280,765301.435.5this study
* The sample used for phylogenetic analysis at species level.
Table 2. Comparison of characteristics in the alignments of unfiltered and filtered (-gb) matrices of the plastid genome (CP), the 26 isolated mitochondrial genes (MT), and the nuclear ribosomal DNA cistron (nrDNA) across Torreya samples.
Table 2. Comparison of characteristics in the alignments of unfiltered and filtered (-gb) matrices of the plastid genome (CP), the 26 isolated mitochondrial genes (MT), and the nuclear ribosomal DNA cistron (nrDNA) across Torreya samples.
DatasetNo. of SamplesLength (bp)Length (bp) *Variable Sites (%) *PI Sites (%) *Identical Sites (%) *
CP40145,775140,7872561 (1.82%)2063 (1.47%)138,226 (98.18%)
CP-gb40135,852135,8522258 (1.66%)1860 (1.37%)133,594 (98.34%)
MT2721,49321,38514 (0.07%)7 (0.03%)21,371 (99.93%)
MT-gb2721,30321,30313 (0.06%)6 (0.03%)21,290 (99.94%)
nrDNA286137611552 (0.85%)44 (0.72%)6063 (99.15%)
nrDNA-gb286100610052 (0.85%)44 (0.72%)6048 (99.15%)
* The information of aligned length, variable sites, parsimony-information (PI) sites, and identical sites of Torreya (excluding two samples of Amentotaxus).
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Mo, Z.-Q.; Wang, J.; Möller, M.; Yang, J.-B.; Gao, L.-M. Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants. Int. J. Mol. Sci. 2023, 24, 13216. https://doi.org/10.3390/ijms241713216

AMA Style

Mo Z-Q, Wang J, Möller M, Yang J-B, Gao L-M. Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants. International Journal of Molecular Sciences. 2023; 24(17):13216. https://doi.org/10.3390/ijms241713216

Chicago/Turabian Style

Mo, Zhi-Qiong, Jie Wang, Michael Möller, Jun-Bo Yang, and Lian-Ming Gao. 2023. "Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants" International Journal of Molecular Sciences 24, no. 17: 13216. https://doi.org/10.3390/ijms241713216

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