Abstract
The genus Cucumis contains 52 species, including two economically significant crops, cucumber and melon, as well as other important species. Cucumis anguria var. anguria is a wild relative of C. melon, native to Africa. Cucumis anguria is rich in vitamins and minerals in gherkin fruits and carries broad-spectrum resistance to multiplex biotic and abiotic stress, such as powdery mildew, fusarium wilt, and meloidogyn incognita. Cucumis anguria provides a valuable gene pool for crop improvement of Cucumis crops. In this study, the complete chloroplast (cp) genome sequence of C. anguria was determined using next-generation sequencing. The entire cp genome was determined to be 156,577 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 85,971 and 18,100 bp, respectively, which were separated by a pair of 26,253 bp inverted repeat (IR) regions. The genome contained 134 genes, including 88 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene infA. The overall GC content of the genome is 37.0%. A phylogenetic tree reconstructed by 48 chloroplast genomes reveals that C. anguria is a separate branch in Cucumis.
Keywords: Cucumis anguria var. anguria, complete chloroplast genome, phylogenetic analysis, Cucurbitaceae
The genus Cucumis contains 52 species, including two economically significant crops, cucumber and melon, as well as other important species. Cucumis anguria var. anguria is a wild relative of C. melon, native to Africa (Kerje and Grum 2000). Cucumis anguria is rich in vitamins and minerals in gherkin fruits and carries broad-spectrum resistance to multiplex biotic and abiotic stress, such as powdery mildew, fusarium wilt, and meloidogyn incognita. Cucumis anguria provides a valuable gene pool for crop improvement of Cucumis crops. However, genetic relationships between C. anguria and other melon species on genomes level have not been studied. So, it is necessary to develop genomic resources for C. anguria to provide basic intragenic information for further study on phylogeny and breeding for genus Cucumis.
The total genomic DNA was extracted from the fresh leaves of C. anguria (Gaolan County, Gansu, China, 36.6 N, 103.38E) using the DNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). The voucher specimen was deposited at Gansu Academy of Agricultural Sciences (2016Y25). The whole genome sequencing was conducted by Genepioneer Biotechnologies Inc. (Nanjing, China) on the Illumina Hiseq 4000 Sequencing System (Illumina, Hayward, CA, USA). The filtered sequences were assembled using the SPAdes assembler 3.10.0 (Bankevich et al. 2012). Annotation was performed using the DOGMA (Wyman et al. 2004). All the tRNA sequences were confirmed using the web-based online tool, tRNAScan-SE (Schattner et al. 2005) with default settings to corroborate tRNA.
The plastome of C. anguria was determined to comprise double-stranded, circular DNA of 156,577 bp containing two inverted repeat (IR) regions of 26,253 bp each, separated by large single-copy (LSC) and small single-copy (SSC) regions of 85,971 and 18,100 bp, respectively (NCBI acc. no. MN807280). The genome contained 134 genes, including 88 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene infA. The eight protein-coding genes, seven tRNA genes, and four rRNA genes were duplicated in the IR region. Seventeen genes contained two exons and four genes (clpP and ycf3 and two rps12) contained three exons. The overall GC content of C. anguria cp genome is 37.0% and the corresponding values in LSC, SSC, and IR regions are 34.7, 31.7, and 42.6%, respectively.
To investigate its taxonomic status, whole chloroplast genomes from 21 Cucumis plants and two outgroup plants (Coccinia grandis and Carica papaya) were aligned by MAFFT version 7 (Katoh and Standley 2013). A maximum likelihood (ML) was reconstructed based on FastTree version 2.1.10 (Price et al. 2010). The ML phylogenetic tree shows that Cucumis anguria is a separate branch in Cucumis, with bootstrap support values of 100% (Figure 1).
Figure 1.
Maximum-likelihood phylogenetic tree for Cucumis anguria based on whole chloroplast genomes from 21 Cucumis plants and two outgroup plant (Coccinia grandis and Carica papaya) and the support values are shown at the branches.
Funding Statement
This research was supported by The National Natural Science Foundation of China [31960523], The National Natural Science Foundation of China [31471896], Technology Support Project of the GAAS [2017GAAS48], Technology Support Project of the GAAS [2019GAAS06], The National Key Research and Development Program of China [2019YFD1000300-11] and The Open Projects of Key Labor [NYB-201907-03].
Disclosure statement
No potential conflict of interest was reported by the authors.
References
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: anew genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Katoh K, Standley D M. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability[J]. Mol Biol Evol. 30(4):772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kerje T, Grum M. 2000. The origin of melon, Cucumis melo: a review of the literature. Acta Hortic. 510:37–44. [Google Scholar]
- Price M N, Dehal P S, Arkin A P. 2010. FastTree 2–approximately maximum-likelihood trees for large alignments[J]. PLoS One. 5(3):e9490. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schattner P, Brooks AN, Lowe TM. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33(Web Server issue):W686–W689. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wyman S K, Jansen R K, Boore J L. 2004. Automatic annotation of organellar genomes with DOGMA[J]. Bioinformatics. 20(17):3252–3255. [DOI] [PubMed] [Google Scholar]