Abstract
Sea buckthorn (Hippophae rhamnoides), a hardy deciduous shrub of the Elaeagnaceae family, grows wild at high altitudes in Asia and Europe and is known for its excellent nutritional, medicinal, and ecological value. However, research on its chloroplast genome is limited. In this study, we sequenced, assembled, and annotated the chloroplast genomes of four subspecies of H. rhamnoides. The structure, nucleotide diversity, simple and long repeat sequence sites, and codon bias of their chloroplast genomes were compared. Their chloroplast genomes (size range 156,185–156,510 bp) consisted of a pair of inverted repeats (IR) sequences (26,658–26,664 bp) separating a small single-copy region (19,025–19064 bp) from a large single-copy region (83,842–84,118 bp). Gene order, IR boundaries, codon usage, and repetitive sequence distribution showed similarities across the four genomes. Except for H. rhamnoides subsp. mongolica ‘wulanshalin’, which was missing the matK gene, the subspecies contained 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. We also uncovered 373 cpSSRs, 175 long repeat sequences, and 9 regions with high variability worth substantiation in future population genetics research. Meanwhile, a phylogenetic tree of the Elaeagnaceae family was constructed from CDSs, showing that all Hippophae taxa were clustered in the same group and formed a sister clade with Elaeagnus taxa. Among the Hippophae taxa, H. gyantsensis, H. neurcar, and H. salicifolia were grouped, but H. tibetana was clustered with H. rhamnoides. The findings of this research will be helpful for further investigations on resource protection and the taxonomic classification of sea buckthorn.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Amiryoussefi A, Hyovnen J, Poczai P (2018) IR scope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34(17):3030–3031. https://doi.org/10.1093/bioinformatics/bty220
Andrews S (2011) Fast QC: A quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Birky CW, Maruyama T, Fuerst P (1983) An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103(3):513–527
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu204
Chi XF, Zhang FQ, Dong Q, Chen SL (2020) Insights into comparative genomics, codon usage bias, and phylogenetic relationship of species from Biebersteiniaceae and Nitrariaceae based on complete chloroplast genomes. Plants 9(11):1605. https://doi.org/10.3390/plants9111605
Dhafer AA, Samaila SY, Enas JA, Abidina A (2020) Complete chloroplast genome sequence of Barleria prionitis, comparative chloroplast genomics and phylogenetic relationships among Acanthoideae. BMC Genomics. https://doi.org/10.1186/s12864-021-07427-2
Downie SR, Jansen RK (2015) A comparative analysis of whole plastid genomes from the apiales: expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Syst Bot 40(1):336–351. https://doi.org/10.1600/036364415X686620
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32(W):273–279. https://doi.org/10.1093/nar/gkh458
Gâtlan AM, Gutt G (2021) Sea buckthorn in plant based diets. An analytical approach of sea buckthorn fruits composition: nutritional value, applications, and health benefits. Int J Environ Res Public Health 18(17):8986. https://doi.org/10.3390/ijerph18178986
Gong L, Ding XX, Guan W, Zhang DC, Zhang J et al (2022) Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC Plant Biol 22(1):520. https://doi.org/10.1186/s12870-022-03898-x
Guo RX, Guo XB, Li Tong FuX, Liu RH (2017) Comparative assessment of phytochemical profiles, antioxidant and antiproliferative activities of Sea buckthorn (Hippophae rhamnoides L.) berries. Food Chem 221:997–1003. https://doi.org/10.1016/j.foodchem.2016.11.063
Guo S, Liao XJ, Chen SY, Liao BS, Guo YM (2022) A Comparative analysis of the chloroplast genomes of four Polygonum medicinal plants. Front Genet 13:764534. https://doi.org/10.3389/fgene.2022.764534
He Y, Xiao HT, Deng C, Xiong L, Yang J (2016) The complete chloroplast genome sequences of the medicinal plant Pogostemon cablin. In J Mol Sci 17(6):820. https://doi.org/10.3390/ijms17060820
Huang Q (2007) Hippophae breeding and cultivation. Science Press, Beijing
Huo YM, Gao LM, Liu BJ, Yang YY, Kong SP et al (2019) Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses. Sci Rep 9(1):12250. https://doi.org/10.1038/s41598-019-48708-x
Huang YY, Yang ZR, Huang S, An WL, Li J et al (2019) Comprehensive analysis of Rhodomyrtus tomentosa chloroplast genome. Plants-Basel 8(4):89. https://doi.org/10.3390/plants8040089
Huang Q (2004) Hybrid dominance of sea buckthorn and hybrid seed orchard establishment. Hippophae 17(3):1–4
Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW et al (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 104(49):19369–19374
Jin JJ, Yu WB, Yang JB, Song Y, de Pamphilis CW et al (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21(1):1–31. https://doi.org/10.1186/s13059-020-02154-5
Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. https://doi.org/10.1093/molbev/mst010
Kumar B, Choudhary M, Kumar P, Kumar K, Kumar S et al (2022) Population structure analysis and association mapping for turcicum leaf blight resistance in tropical maize using SSR markers. Genes 13(4):618. https://doi.org/10.3390/genes13040618
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J et al (2001) Reputer: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29(22):4633–4642. https://doi.org/10.1093/nar/29.22.4633
Lee KJ, Lee GA, Lee JR, Sebastin R, Shin MJ et al (2019) Genetic diversity of sweet potato (Ipomoea batatas L. Lam) Germplasms collected worldwide using chloroplast SSR markers. Agronomy-Basel 9(11):752. https://doi.org/10.3390/agronomy9110752
Letunic I, Bork P (2021) Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49(W1):293–296. https://doi.org/10.1093/nar/gkab301
Li H, Ruan CJ, Teixeira da Silva JA (2009) Identification and genetic relationship based on ISSR analysis in a germplasm collection of sea buckthorn (Hippophae L.) from China and other countries. Sci Hortic 123(2):263–271. https://doi.org/10.1016/j.scienta.2009.08.007
Lian YS, Chen XL (1996) Systematic classification of hippophae. Hippophae 9(1):15–24
Ma QG, Guan Y, Song ZP, Dong JH, Wei RR (2022) Isolation and characterization of auronlignan derivatives with hepatoprotective and hypolipidemic activities from the fruits of Hippophae rhamnoides L. Food Func 13(14):7750–7761. https://doi.org/10.1039/D2FO01079H
Ma YH, Ye GS, Xiang QS, Gao Y, Yang CJ et al (2014) Phylogenetic relationships of sea buckthorn based on ITS sequences. Chin J Appl Ecol 25(10):2985–2990. https://doi.org/10.13287/j.1001-9332.20140731.009
Mehmood F, Abdullah I, Shahzadi I, Ahmed I, Waheed MT et al (2020) Characterization of Withania Somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics 112(2):1522–1530. https://doi.org/10.1016/j.ygeno.2019.08.024
Neuhaus HE, Emes MJ (2000) Nonphotosynthetic metabolism in plastids. Annu Rev Plant Physiol Plant Mol Biol 51(1):111–140. https://doi.org/10.1146/annurev.arplant.51.1.111
Nie X, Den LP, Du X et al (2014) Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family. Plant Mol Biol Rep 32(4):828–840. https://doi.org/10.1007/s11105-013-0691-z
Park I, Yang S, Choi G, Kim WJ, Moon BC (2017) The complete chloroplast genome sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and development of molecular markers for distinguishing species in the Aconitum Subgenus Lycoctonum. Molecules 22(11):2012. https://doi.org/10.3390/molecules22112012
Quax TEF, Claassens NJ, Soll D, van der Oost J (2015) Codon bias as a means to fine-tune gene expression. Mol Cell 59(2):149–161. https://doi.org/10.1016/j.molcel.2015.05.035
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P et al (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34(12):3299–3302. https://doi.org/10.1093/molbev/msx248
Song Y, Chen Y, Lv J, Xu J, Zhu S et al (2017) Development of chloroplast genomic resources for Oryza species discrimination. Front Plant Sci 8:1854. https://doi.org/10.3389/fpls.2017.01854
Shi LC, Chen HM, Jiang M, Wang LQ, Wu X et al (2019) CPGAVAS2, an integrated plastome sequence annotator and analyser. Nucleic Acids Res 47(W1):W65–W73. https://doi.org/10.1093/nar/gkz345
Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19(1):149–168. https://doi.org/10.1007/BF00015612
Wang J (2020) Study on the evolution of chloroplast genome of Hippophae. Dissertation, Chinese Academy of Forestry
Wang ZJ, Xu BB, Li B, Zhou QQ, Wang GY (2020) Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ 8:e8251. https://doi.org/10.7717/peerj.8251
Wu (2004) Experimental study on regionalisation of introduced Russian sea buckthorn varieties. Hippophae 17(2):7–10
Wick RR, Schultz MB, Zobel J, Holt KE (2015) Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31(20):3350–3352. https://doi.org/10.1093/bioinformatics/btv383
Yao XH, Tang P, Li ZZ, Li DW, Liu YF et al (2015) The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. PLoS ONE 10(6):e129347. https://doi.org/10.1371/journal.pone.0129347
Yan HQ, Qi HS, Li Y, Wu YG, Wang Y et al (2022) Assessment of the genetic relationship and population structure in oil-tea camellia species using simple sequence repeat (SSR) markers. Genes 13(11):2162. https://doi.org/10.3390/genes13112162
Yuan W (1988) Hippophae rhamnoides subsp. yunnanensis resources and their ecological distribution. J Yunnan Agric Univ 3(02):218–219. https://doi.org/10.16211/j.issn.1004-390x(n).1988.02.022
Zeng YJ, Shen LW, Chen SQ, Qu S, Hou N (2023) Codon usage profiling of chloroplast genome in Juglandaceae. Forests 14(2):378. https://doi.org/10.3390/f14020378
Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J et al (2020) PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour 20(1):348–355. https://doi.org/10.1111/1755-0998.13096
Zhang QX, Li J, Yang Y, Xu HH (2023) A new map of the chloroplast genome of Hippophae based on inter and intraspecific variation analyses of 13 accessions belonging to eight Hippophae species. Braz J Bot 46(2):367–382. https://doi.org/10.1007/s40415-023-00890-z
Zheng SY, Poczai P, Hyvönen J, Tang J, Amiryousefi A (2020) Chloroplot: an online program for the versatile plotting of organelle genomes. Front Genet. https://doi.org/10.3389/fgene.2020.576124
Funding
This research was supported by the Starting Fund for Doctoral Research of Shanxi Agricultural University (2015YJ15 and 2015YJ16), the Shanxi Province Applied Basic Research Program (201901D211360), Teaching Reform Innovation Program for Higher Education Institutions in Shanxi Province of China (No. J202303045), and the Shanxi Province Basic Research Program (202103021224141).
Author information
Authors and Affiliations
Contributions
X.Q. and H.Y.Z. conceived and designed the project. W.R.Q. and W.X.J. analysed the data. W.R.Q. drafted the original manuscript. L.Z.H. and X.Q. provided financial support and reviewed and revised the paper.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Wang, R., Wang, X., Liu, Z. et al. Comparative chloroplast genome analysis of four Hippophae rhamnoides subspecies and its phylogenetic analysis. Genet Resour Crop Evol (2023). https://doi.org/10.1007/s10722-023-01788-1
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10722-023-01788-1