SpringerLink
Log in

The complete chloroplast genome of white towel gourd (Luffa cylindrica) and phylogenetic analysis

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

White towel gourd (Luffa cylindrica) is an important cultivated vegetable and economic plant belong to the Cucurbitaceae family. In this study, the complete cp genome of L. cylindrica was successfully sequenced using the Illumina NovaSeq 6000 platform, and compared with its closely related Cucurbitaceae species. The complete cp genome of L. cylindrica had a length of 157,296 bp. The cp genome exhibited a typical quadripartite structure, including a pair of inverted repeat (IRa and IRb) regions (26,287 bp), a large single-copy (LSC) region (86,321 bp), and a small single-copy (SSC) region (18,401 bp). The genome encoded 131 genes, consisting of 37 tRNA genes (tRNAs), eight rRNA genes (rRNAs), and 86 protein-coding genes (CDS). A total of 31 codons and 270 simple sequence repeats (SSRs) were found in the cp genome of L. cylindrica. Ka/Ks analysis showed purification selection in the most of coding genes. However, the ycf2, accD, atpE, rps4, clpP, rpl32 and ndhG genes of L. lcylindrica were influenced by positive selection. Seven highly divergent regions were the ycf1, rps12, rpl22, accD, clpP, petL and rps19 genes, which located at the LSC and SSC regions. Phylogenetic analysis revealed that L. aegyptiaca (OQ810000.1) was closely related to L. Cylindrica. Our results of the cp genome of L. cylindrica could provide available information for further species identification, classification, molecular marker, evolution and phylogeny of Cucurbitaceae plants.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Alverson AJ, Wei XX, Rice DW et al (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 27(6):1436–1448

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Amiryousefi A, Hyvönen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34(17):3030–3031

    Article  PubMed  CAS  Google Scholar 

  • Arise RO, Idi JJ, Mic-Braimoh IM et al (2019) In vitro Angiotesin-1-converting enzyme, α-amylase and α-glucosidase inhibitory and antioxidant activities of Luffa cylindrical (L.) M. Roem seed protein hydrolysate. Heliyon 5(5):97–101

    Article  Google Scholar 

  • Azeez MA, Bello OS, Adedeji AO (2013) Traditional and medicinal uses of Luffa cylindrica: a review. J Med Plants Stud 1(5):102–111

    Google Scholar 

  • Bellgard M, Schibeci D, Trifonov E et al (2001) Early detection of G+ C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J Mol Evol 53:465–468

    Article  PubMed  CAS  Google Scholar 

  • Biswas KK, Palchoudhury S, Chakraborty P et al (2019) Codon usage bias analysis of citrus tristeza virus: higher codon adaptation to Citrus reticulata host. Viruses 11(4):331

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chakraborty S, Yengkhom S, Uddin A (2020) Analysis of codon usage bias of chloroplast genes in Oryza species: codon usage of chloroplast genes in Oryza species. Planta 252:1–20

    Article  Google Scholar 

  • Chen Z, Liu Q, **ao Y et al (2023) Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genet 64(3):419–429

    Article  PubMed  CAS  Google Scholar 

  • Cheng H, Kong WP, Zhang MM et al (2020) The complete chloroplast genome of Cucumis melo L. ‘Shengkaihua’ (Cucurbitaceae) and its phylogenetic implication. Mitochondrial DNA Part B 5(2):1253–1254

    Article  Google Scholar 

  • Chu D, Wei L (2019) Characterizing the heat response of Arabidopsis thaliana from the perspective of codon usage bias and translational regulation. J Plant Physiol 240:153012

    Article  PubMed  CAS  Google Scholar 

  • Dairo FAS, Aye PA, Oluwasola TA (2007) Some functional properties of loofah gourd (Luffa cylindrica L., MJ Roem) seed. J Food Agric Environ 5(1):97

    CAS  Google Scholar 

  • Daniell H, Chan HT, Pasoreck EK (2016) Vaccination via chloroplast genetics: affordable protein drugs for the prevention and treatment of inherited or infectious human diseases. Annu Rev Genet 50:595–618

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Deng J, Li W, Xu W et al (2021) Correlation and the concentrations of Pb, Cd, Hg and As in vegetables and soils of Chongqing, China. Environ Geochem Health 43:2357–2376

    Article  PubMed  CAS  Google Scholar 

  • Feng C, Wang J, Zhao Y et al (2015) Technology and application of identification and evaluation for towel gourd germplasm resources. Bot Res 4(3):33–38

    Google Scholar 

  • Fu Y, Brookfield H, Guo H et al (2009) Smallholder rubber plantation expansion and its impact on local livelihoods, land use and agrobiodiversity, a case study from Daka, **shuangbanna, southwestern China. Int J Sustain Dev World Ecol 16(1):22–29

    Article  Google Scholar 

  • Han C, Zuo J, Wang Q et al (2014) Effects of chitosan coating on postharvest quality and shelf life of sponge gourd (Luffa cylindrica) during storage. Sci Hortic 166:1–8

    Article  CAS  Google Scholar 

  • Han H, Qiu R, Liu Y et al (2022) Analysis of chloroplast genomes provides insights into the evolution of Agropyron. Front Genet 13:832809

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Huang Y, Li J, Yang Z et al (2022) Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species. BMC Plant Biol 22(1):1–15

    Article  CAS  Google Scholar 

  • Iriarte A, Lamolle G, Musto H (2021) Codon usage bias: an endless tale. J Mol Evol 89(9–10):589–593

    Article  PubMed  CAS  Google Scholar 

  • Jansen RK, Ruhlman TA (2012) Plastid genomes of seed plants. Genomics Chloroplasts Mitochondria. https://doi.org/10.1007/978-94-007-2920-9_5

    Article  Google Scholar 

  • Jiang D, Cai X, Gong M et al (2023) Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC Genomics 24(1):30

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim JS, Jung JD, Lee JA et al (2006) Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25:334–340

    Article  PubMed  CAS  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li E, Liu K, Deng R et al (2023) Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae). BMC Plant Biol 23(1):1–14

    Article  CAS  Google Scholar 

  • Lian C, Yang H, Lan J et al (2022) Comparative analysis of chloroplast genomes reveals phylogenetic relationships and intraspecific variation in the medicinal plant Isodon rubescens. PLoS ONE 17(4):e0266546

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liang D, Wang H, Zhang J et al (2022) Complete chloroplast genome sequence of Fagus longipetiolata Seemen (Fagaceae): genome structure, adaptive evolution, and phylogenetic relationships. Life 12(1):92

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452

    Article  PubMed  CAS  Google Scholar 

  • Loewe L, Charlesworth B, Bartolomé C, Noel V (2006) Estimating selection on nonsynonymous mutations. Genetics 172:1079–1092

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lohse M, Drechsel O, Bock R (2007) OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–274

    Article  PubMed  CAS  Google Scholar 

  • Lu G, Zhang K, Que Y et al (2023) Assembly and analysis of the first complete mitochondrial genome of Punica granatum and the gene transfer from chloroplast genome. Front Plant Sci 14:1132551

    Article  PubMed  PubMed Central  Google Scholar 

  • Matthee CA, Eick G, Willows-Munro S et al (2007) Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics. Mol Phylogenet Evol 42(3):827–837

    Article  PubMed  CAS  Google Scholar 

  • Mayor C, Brudno M, Schwartz JR et al (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16(11):1046–1047

    Article  PubMed  CAS  Google Scholar 

  • McGinnis S, Madden TL (2004) BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res 32(suppl_2):W20–W25

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Niu Y, Qin Q, Dong Y et al (2023) Chloroplast Genome structure and phylogenetic analysis of 13 lamiaceae plants in Tibet. Front Biosci-Landmark 28(6):110

    Article  CAS  Google Scholar 

  • Pląder W, Yukawa Y, Sugiura M et al (2007) The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis. Cell Mol Biol Lett 12(4):584–594

    Article  PubMed  PubMed Central  Google Scholar 

  • Shaw J, Lickey EB, Beck JT et al (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92(1):142–166

    Article  PubMed  CAS  Google Scholar 

  • Shi W, Hu S, Song W et al (2023) Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus (Rhamnaceae). Physiol Mol Biol Plants 29(6):855–869

    Article  PubMed  CAS  Google Scholar 

  • Sohrab SS, Mandal B, Pant RP et al (2003) First report of association of tomato leaf curl virus-new delhi with yellow mosaic disease of Luffa cylindrica in india. Plant Dis 87(9):1148–1148

    Article  PubMed  CAS  Google Scholar 

  • Song W, Ji C, Chen Z et al (2022) Comparative analysis the complete chloroplast genomes of nine Musa species: genomic features, comparative analysis, and phylogenetic implications. Front Plant Sci 13:832884

    Article  PubMed  PubMed Central  Google Scholar 

  • Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688–2690

    Article  PubMed  CAS  Google Scholar 

  • Tang D, Wei F, Cai Z et al (2021) Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis benth. Dev Genes Evol 231:1–9

    Article  PubMed  CAS  Google Scholar 

  • Wang D, Zhang Y, Zhang Z et al (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinform 8(1):77–80

    Article  CAS  Google Scholar 

  • Wang X, Bai S, Zhang Z et al (2023) Comparative analysis of chloroplast genomes of 29 tomato germplasms: genome structures, phylogenetic relationships, and adaptive evolution. Front Plant Sci 14:1179009

    Article  PubMed  PubMed Central  Google Scholar 

  • Wanichthanarak K, Nookaew I, Pasookhush P et al (2023) Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae. BMC Plant Biol 23(1):59

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wong EHM, Smith DK, Rabadan R et al (2010) Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol Biol 10(1):1–14

    Article  Google Scholar 

  • Wu HY, Wong KH, Kong BLH et al (2022) Comparative analysis of chloroplast genomes of Dalbergia species for identification and phylogenetic analysis. Plants 11(9):1109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wu L, Fan P, Zhou J et al (2023) Gene losses and homology of the chloroplast genomes of Taxillus and Phacellaria species. Genes 14(4):943

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • **ao Z, Tao Z, Jia Y et al (2018) Comparative analyses of chloroplast genomes of Cucurbitaceae species: lights into selective pressures and phylogenetic relationships. Molecules 23(9):2165. https://doi.org/10.3390/molecules23092165

    Article  CAS  Google Scholar 

  • **e YP, Yang GG, Zhang C et al (2023) Comparative analysis of chloroplast genomes of endangered heterostylous species Primula wilsonii and its closely related species. Ecol Evol 13(1):e9730

    Article  PubMed  PubMed Central  Google Scholar 

  • Yanfei N, Tai S, Chunhua W et al (2023) Complete chloroplast genome sequences of the medicinal plant Aconitum transsectum (Ranunculaceae): comparative analysis and phylogenetic relationships. BMC Genomics 24(1):1–15

    Article  Google Scholar 

  • Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32–43

    Article  PubMed  CAS  Google Scholar 

  • Yang L, Deng S, Zhu Y et al (2023) Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny. BMC Plant Biol 23(1):1–20

    Article  CAS  Google Scholar 

  • Yundaeng C, Nawae W, Naktang C et al (2020) Chloroplast genome data of Luffa acutangula and Luffa aegyptiaca and their phylogenetic relationships. Data in Brief, 33: 106470. https://doi.org/10.1016/j.dib.2020.106470

    Article  CAS  Google Scholar 

  • Zhang X, Zhou T, Kanwal N et al (2017) Completion of eight Gynostemma BL. (Cucurbitaceae) chloroplast genomes: characterization, comparative analysis, and phylogenetic relationships. Front Plant Sci 8:1583

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang C, Zhu Q, Liu S et al (2018) The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae). Mitochondrial DNA Part B 3(2):717–718

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Shi M, Ji J et al (2019) Gut microbiota determines the prevention effects of Luffa cylindrical (L.) ROEM supplementation against obesity and associated metabolic disorders induced by high-fat diet. FASEB J 33(9):10339–10352

    Article  PubMed  CAS  Google Scholar 

  • Zhang P, Xu W, Lu X et al (2021) Analysis of codon usage bias of chloroplast genomes in Gynostemma species. Physiol Mol Biol Plants 27:2727–2737

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang Y, Shen Z, Meng X et al (2022) Codon usage patterns across seven Rosales species. BMC Plant Biol 22(1):65

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Si Y, Zhao R et al (2023) Complete chloroplast genome and phylogenetic relationship of Nymphaea nouchali (Nymphaeaceae), a rare species of water lily in China. Gene 858:147139

    Article  PubMed  CAS  Google Scholar 

  • Zhao Y, Yin J, Guo H et al (2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Front Plant Sci 5:696

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou M, Li X (2009) Analysis of synonymous codon usage patterns in different plant mitochondrial genomes. Mol Biol Rep 36:2039–2046

    Article  PubMed  CAS  Google Scholar 

  • Zhu Q, Gao P, Liu S et al (2016a) Comparative analysis of single nucleotide polymorphisms in the nuclear, chloroplast, and mitochondrial genomes in identification of phylogenetic association among seven melon (Cucumis melo L.) cultivars. Breed Sci 66(5):711–719

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu Q, Cui H, Zhao Y et al (2016b) The complete chloroplast genome sequence of the Citrullus lanatus L. Subsp. Vulgaris (Cucurbitaceae). Mitochondrial DNA Part B 1(1):943–944

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhu Y, Zhang X, Yan S et al (2023) SSR identification and phylogenetic analysis in four plant species based on complete chloroplast genome sequences. Plasmid 125:102670

    Article  PubMed  CAS  Google Scholar 

Download references

Funding

This work was supported by Hunan Provincial Science and Technology Commissioner Service Rural Revitalization Project (Grant Numbers 2022NK4218).

Author information

Authors and Affiliations

  1. College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 417000, China

    Yihui Gong, Yuanyuan Wei, Guihua Zhou, Yanglan Ou & Canmei Zhang

  2. **angtan Agricultural Science Research Institute, **angtan, 411100, China

    Peng Li

Authors
  1. Yihui Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuanyuan Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Guihua Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yanglan Ou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Canmei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Peng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

YG and PL conceived and designed the study. YG, YW, and GZ performed the experiments and data analysis. YG, YO, and CZ contributed materials collection. YG and PL wrote and revised the paper. All authors approved the final manuscript.

Corresponding authors

Correspondence to Yihui Gong or Peng Li.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Consent for publication

The corresponding authors declares, on behalf of all co-authors, that the work described is original, previously unpublished research, and not under consideration for publication elsewhere.

Ethics approval

The experiments in this study comply with the current laws of China.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 126 kb)

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.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gong, Y., Wei, Y., Zhou, G. et al. The complete chloroplast genome of white towel gourd (Luffa cylindrica) and phylogenetic analysis. Genet Resour Crop Evol (2024). https://doi.org/10.1007/s10722-023-01842-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10722-023-01842-y

Keywords

Search

Navigation