The complete plastome sequence of Momordica cochinchinensis (Cucurbitaceae)

Abstract Momordica cochinchinensis (Lour.) Spreng. is an important medicinal plant that is used to treat various diseases in South and Southeast Asia. In this study, the complete plastome of M. cochinchinensis was sequenced and found to exhibit a total length of 158,955 bp, with a large single copy (LSC) region of 87,924 bp and a small single copy (SSC) region of 18,479 bp, as well as with two inverted repeats (IRs) that were both 26,726 bp in length. In total, 129 genes were detected, comprising 86 protein-encoding genes, 8 ribosomal RNA (rRNA) genes, and 35 transfer RNA (tRNA) genes. Furthermore, the inferred phylogenetic tree confirmed that M. cochinchinensis belongs to the genus Momordica in the Cucurbitaceae family. The research results will be used for authenticating M. cochinchinensis plant materials and for analyzing the genetic diversity and phylogenetic relationships in Momordica.


Introduction
Momordica cochinchinensis (Lour.) Spreng. 1826, commonly known as Gac fruit, sweet gourd, baby jackfruit, or cochinchin gourd (Bootprom et al. 2015), is a perennial dioecious cucurbit plant that originated in South and Southeast Asia and that is widely sold for dietary and medicinal purposes (Vuong et al. 2006). Momordica cochinchinensis is highly rich in lycopene and beta-carotene, vitamin E, fatty acids, flavonoids, phenolic acids, and trypsin inhibitors (Chuyen et al. 2015). These phytochemicals are associated with many significant pharmacological activities, such as provitamin A, antioxidant, antimicrobial, antiulcer, and anticancer activities (Jayanthi et al. 2020). The pulp of the seed or aril of the ripe fruit is usually utilized as a natural colorant and food additive because of its bright red color and rich nutritional content (Bootprom et al. 2013). The genetic diversity of Gac fruit is also important for germplasm exploration and selective breeding; unfortunately, there is a lack of genetic information about the underutilized crop (Bootprom et al. 2015;Jayanthi et al. 2020). The complete plastome of many plants has been sequenced, and DNA molecular markers have been developed and used for the identification of species and phylogenetic analysis (Li et al. 2022). Until now, there has been no research on the use of the whole plastome of M. cochinchinensis as a molecular genetic resource. Therefore, the current research was conducted to publish the whole chloroplast genome of M. cochinchinensis in order to enhance the molecular investigation of germplasm, genetic diversity, and phylogenetic relationships.

Materials and methods
Momordica cochinchinensis seeds were collected at Fangchenggang (21 46 0 8.87 00 N, 108 21 0 12.31 00 ), Guangxi, China, and seedlings of M. cochinchinensis (voucher number: QZ06MC, Figure 1) were grown at the ecological garden of Jiangxi Agricultural University, Nanchang, China (contact person: Qianglong Zhu, longzhu2011@126.com). Young and healthy plant leaves were sampled, and total genomic DNA (gDNA) was isolated according to the modified cetyltrimethylammonium bromide (CTAB) method (Porebski et al. 1997). Approximately, 15 lg of gDNA was isolated and delivered to the Beijing Genomics Institute (BGI) for genomic sequencing by using the BGISEQ-500 Platform (Shenzhen, China). Nearly 0.5 gigabytes (Gb) of clean paired reads were obtained after checking the sequence data quality. Plasmidspades.py was used to assemble the draft genome sequence (Bankevich et al. 2012), and the top scaffolds with high coverage and length for the plastome were then extracted, ordered, and combined into a plastome sequence draft according to the reference plastome of Momordica charantia (NC_036807.1). GapCloser was used to repair the gaps within the plastome sequence draft, and the integrality and quality of the plastome sequence were checked and improved by referenceguided mapping using Burrows-Wheeler Aligner (BWA), SAMtools and Integrative Genomics Viewer (IGV). The average and minimum read mapping depths of the assembled genome were 58Â and 18Â ( Figure S1), respectively. Finally, the genes in the plastome sequence were annotated using GeSeq and CPGAVAS2 (Chang et al. 2012;Tillich et al. 2017). The annotated results were manually reviewed and corrected with Sequin software. The circular M. cochinchinensis plastome map was drawn using CPGView (Liu et al. 2023). For phylogenetic analysis, complete plastome sequences were aligned by using Multiple Alignment using Fast Fourier Transform (MAFFT, v7.463) (Rozewicki et al. 2019), and a phylogenetic tree was constructed based on the sequence alignment by Molecular Evolutionary Genetics Analysis (MEGA) (v11) with the maximum-likelihood (ML) method (Tamura et al. 2021).

Results
The length of the complete M. cochinchinensis plastome (ON597626) was 158,955 bp with 36.22% GC content ( Figure  2), contained the LSC (87,924 bp) and SSC (18,479 bp) regions and two IRs that were both 26,726 bp in length, and showed a typical quadripartite structure. However, a total of 129  genes were identified as being distributed in different regions of the plastome, including 86 protein-encoding genes, 35 tRNA genes, and 8 rRNA genes. Of these genes, 13 protein-encoding and 7 tRNA genes harbored at least two exons.
To date, there are two complete plastomes (Momordica charantia and Momordica sessilifolia) in the genus Momordica (Bellot et al. 2020), and approximately, 62 complete plastomes of Cucurbitaceae have been deposited in the NCBI Genome database; these complete plastomes represent 27 genera. To confirm the phylogenetic status of M. cochinchinensis, 30 complete plastome sequences representing the different genera of Cucurbitaceae and an outgroup species (Begonia coptidifolia) were used to infer a phylogenetic tree. The inferred phylogenetic tree suggested that M. cochinchinensis is closely related to M. charantia and M. sessilifolia, and that it belonged to Momordica in the Cucurbitaceae family (Figure 3).
research on phylogenetic relationships in Momordica is necessary and should entail combining molecular markers from plastid and nuclear genomes. Our research results could be used for authenticating M. cochinchinensis and analyzing the genetic diversity and phylogenetic relationships in Momordica.