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Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers

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Abstract

Akebia trifoliata (Lardizabalaceae) is an important medicinal plant with multiple pharmacological effects. However, the lack of genomic information had limited the further excavation and utilization of this plant. An initial survey of the genome A. trifoliata was performed by next-generation sequencing, and then the genome size was inferred by flow cytometry. The whole genome survey of A. trifoliata generated 61.90 Gb of sequence data with approximately 95.51 × coverage. The genome size, heterozygosity and GC content obtained by k-mer analysis were almost 648.07 Mb, 0.72% and 36.11%, respectively. The genome size calculated by flow cytometry was 685.77 Mb, which was consistent with the results of genome survey. A total of 851,957 simple sequence repeats (SSR) were identified in the A. trifoliata genome. Twenty-eight phenotypic traits and thirty pairs of SSR primers were selected for the analysis of the genetic diversity of 43 accessions of cultivated A. trifoliata. The results showed that 216 bands were generated by 30 pairs of SSR primers, of which 189 (87.5%) were polymorphic. In addition, the phenotypes and SSR markers were used for cluster analysis of 43 cultivated accessions. The results of the two clustering methods were partially consistent. The genome survey of A. trifoliata demonstrated that the genome size of this plant was about 648.07 Mb. In the present study, the size and characteristics of the genome of A. trifoliata were reported for the first time, which greatly enriched the genomic resources of A. trifoliata for the further research and utilization.

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Data availability

The genome sequence reads obtained by Illumina Hiseq 2500 are available at NCBI-SRA. The Bioproject accessions number is PRJNA667569, and the Biosample accessions number is SAMN16378157. The Experiment number is SRX9274273/ The Run number is SRR12805495.

References

  1. Chinese Flora Commission (2001) Flora of China. Science Press, China, p 8

    Google Scholar 

  2. National Pharmacopoeia Committee (2020) Chinese pharmacopoeia. China Medical Science and Technology Press, Beijing, p 297

    Google Scholar 

  3. Lu WL, Yang T, Song QJ, Fang ZQ, Pan ZQ, Liang C, Jia DW, Peng PK (2018) Akebia trifoliata (Thunb.) Koidz seed extract inhibits human hepatocellular carcinoma cell migration and invasion in vitro. J Ethnopharmacol 234:204–215. https://doi.org/10.1016/j.jep.11.044

    Article  PubMed  Google Scholar 

  4. Li L, Chen XZ, Yao XH, Tian H, Huang HW (2010) Geographic distribution and resource status of three important Akebia species. J Wuhan Bot Res 28(4):497–506. https://doi.org/10.3724/SP.J.1142.2010.40497

    Article  Google Scholar 

  5. Motalebipour EZ, Kafkas S, Khodaeiaminjan M, Çoban N, Gözel H (2016) Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: development of novel SSR markers and genetic diversity in Pistacia species. BMC Genomics 17(1):998. https://doi.org/10.1186/s12864-016-3359-x

    Article  Google Scholar 

  6. Wang CR, Yan HD, Li J, Zhou SF, Liu T, Zhang XQ, Huang LK (2018) Genome survey sequencing of purple elephant grass (Pennisetum purpureum Schum ‘Zise’) and identification of its SSR markers. Mol Breed 38(7):94. https://doi.org/10.1007/s11032-018-0849-3

    Article  CAS  Google Scholar 

  7. Lu M, An HM, Li LL (2016) Genome survey sequencing for the characterization of the genetic background of rosa roxburghii tratt and leaf ascorbate metabolism genes. PLoS ONE 11(2):e0147530. https://doi.org/10.1371/journal.pone.0147530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Shi LL, Yi SK, Li YH (2018) Genome survey sequencing of red swamp crayfish Procambarus clarkii. Mol Biol Rep 45(5):799–806. https://doi.org/10.1007/s11033-018-4219-3

    Article  CAS  PubMed  Google Scholar 

  9. Zhou W, Li B, Li L, Ma W, Liu YC, Feng SC, Wang ZZ (2018) Genome survey sequencing of Dioscorea zingiberensis. Genome 61(8):567–574. https://doi.org/10.1139/gen-2018-0011

    Article  CAS  PubMed  Google Scholar 

  10. Anju B, Kalpalatha M, Sathya E, Julian J, Umesh R (2019) Characterization of strawberry (Fragaria spp.) accessions by genotyping with SSR markers and phenotyping by leaf antioxidant and trichome analysis. Sci Horticulturae 256:1–7. https://doi.org/10.1016/j.scienta

    Article  Google Scholar 

  11. Da Silva BSR, Sant’Ana GC, Chaves CL et al (2019) Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers. Genetica 147(2):205–216. https://doi.org/10.1007/s10709-019-00064-4

    Article  PubMed  Google Scholar 

  12. Li GQ, Song LX, Jin CQ, Li M, Gong SP, Wang YF (2019) Genome survey and SR analysis of Apocynum venetum. Biosci Rep 39(6):1–11. https://doi.org/10.1042/BSR20190146

    Article  Google Scholar 

  13. Liu WC, Xu YT, Li ZK, Fan J, Yang Y (2019) Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra). Mol Biol Rep 46(6):6087–6098. https://doi.org/10.1007/s11033-019-05044-7

    Article  CAS  PubMed  Google Scholar 

  14. Tuler AC, Carrijo TT, Nóia LR, Ferreira A, Peixoto AL, da Silva Ferreira MF (2015) SSR markers: a tool for species identification in Psidium (Myrtaceae). Mol Biol Rep 42(11):1501–1513. https://doi.org/10.1007/s11033-015-3927-1

    Article  CAS  PubMed  Google Scholar 

  15. Meinke DW, Cherry JM, Dean C, Rounsley SD, Koornneef M (1998) Arabidopsis thaliana: a model plant for genome analysis. Science 282(5389):679–682. https://doi.org/10.1126/science.282.5389.662

    Article  Google Scholar 

  16. Dpooležel J, Binarová P, Lcretti S (1989) Analysis of Nuclear DNA content in plant cells by Flow cytometry. Biol Plant 31(2):113–120. https://doi.org/10.1007/BF02907241

    Article  Google Scholar 

  17. Li RQ, Fan W, Tian G, Zhu H, He L et al (2010) The sequence and de novo assembly of the giant panda genome. Nature 463:311–317. https://doi.org/10.1038/nature08696

    Article  CAS  PubMed  Google Scholar 

  18. Marcais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764–770. https://doi.org/10.1093/bioinformatics/btr011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Varshney RK, Chen W, Li Y et al (2011) Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol 30(1):83–89. https://doi.org/10.1038/nbt.2022

    Article  CAS  PubMed  Google Scholar 

  20. Zhou W, Hu YY, Sui ZH, Fu F, Wang JG, Chang LP, Guo WH, Li BB (2013) Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing. PLoS ONE 8(7):e69909. https://doi.org/10.1371/journal.pone.0069909

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    Article  CAS  Google Scholar 

  22. Salamov AA, Solovyev VV (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10(4):516–522

    Article  CAS  Google Scholar 

  23. Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B (2006) AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res 34:W435-439. https://doi.org/10.1093/nar/gkl200

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kailwaqen J, Hartunq F, Paulini M, Twardziok SO, Grau J (2018) Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinform 19(1):189–201. https://doi.org/10.1186/s12859-018-2203-5

    Article  CAS  Google Scholar 

  25. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 8(8):1494–1512. https://doi.org/10.1038/nprot.2013.084

    Article  CAS  PubMed  Google Scholar 

  26. Tang SY, Lomsadze A, Borodovsky M (2015) Identification of protein coding regions in RNA transcripts. Nucleic Acids Res 43(12):e78. https://doi.org/10.1093/nar/gkv227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kent WJ (2002) BLAT-the BLAST-like alignment tool. Genome Res 12(4):656–664. https://doi.org/10.1101/gr.229202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Marchlerbauer A, Anderson JB, Cherukuri PF et al (2005) CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res 33:D192–D196. https://doi.org/10.1093/nar/gki069

    Article  CAS  Google Scholar 

  29. Boeckmann B, Bairoch A, Apweiler R et al (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31(1):365–370. https://doi.org/10.1093/nar/gkg095

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Tatusov RL, Fedorova ND, Jackson JD et al (2003) The COG database: an updated version includes eukaryotes. BMC Bioinform 4:41. https://doi.org/10.1186/1471-2105-4-41

    Article  Google Scholar 

  31. Dimmer EC, Huntley RP, Alam-Faruque Y et al (2012) The UniProt-GO annotation database in 2011. Nucleic Acids Res 40:D565–D570. https://doi.org/10.1093/nar/gkr1048

    Article  CAS  PubMed  Google Scholar 

  32. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopaedia of genes and genomes. Nucleic Acids Res 28(1):27–30. https://doi.org/10.1093/nar/28.1.27

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Thiel T, Michalek W, Varshney R (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422. https://doi.org/10.1007/s00122-002-1031-0

    Article  CAS  Google Scholar 

  34. Xiong DS, Zhu JT, Li X, Chen XT, Xiong YS (2000) The Karyotype of Akebia trifoliata. Chin Wild Plant Resour 19(6):18–20

    Google Scholar 

  35. Chen RY (2009) Chromosome atlas of major economic plants genome in China. Science Press, China, p 351

    Google Scholar 

  36. Xiao J, Zhao J, Liu MJ, Liu P, Dai L, Zhao ZH (2015) Genome-wide characterization of simple sequence repeat (SSR) loci in Chinese jujube and jujube SSR primer transferability. PLoS ONE 10(5):e0127812. https://doi.org/10.1371/journal.pone.0127812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Velasco R, Zharkikh A, Affourtit J et al (2010) The genome of the domesticated apple (Malus × domestica Borkh). Nat Genet 42(10):833–839. https://doi.org/10.1038/ng.654

    Article  CAS  PubMed  Google Scholar 

  38. Rasch EM (1985) DNA “standards” and the range of accurate DNA estimates by Feulgen absorption microspectrophotometry. Prog Clin Biol Res 196:137–166

    CAS  PubMed  Google Scholar 

  39. Lingohr E, Frost S, Johnson RP (2009) Determination of bacteriophage genome size by pulsed-field gel electrophoresis. Methods Mol Biol 502:19–25. https://doi.org/10.1007/978-1-60327-565-1-3

    Article  CAS  PubMed  Google Scholar 

  40. Zhu DM, Song W, Yang K et al (2012) Flow cytometric determination of genome size for eight commercially important fish species in China. In Vitro Cell Dev Biol Anim 48(8):507–517. https://doi.org/10.1007/s11626-012-9543-7

    Article  PubMed  Google Scholar 

  41. Huo KS, Zhao DL, Chen YL, Zhou ZL, Wang Y, Tang J, Zhu GP, Cao QH (2018) Analysis of genome size and characteristics of salt-tolerant Plant Ipomoeapes-caprae (L.) R.Brown. J Plant Genet Resour 20(3):728–735. https://doi.org/10.13430/j.cnki.jpgr.20180816001

    Article  Google Scholar 

  42. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12(2):R18. https://doi.org/10.1186/gb-2011-12-2-r18

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Bi QX, Zhao Y, Cui YF, Wang LB (2019) Genome survey sequencing and genetic background characterization of yellow horn based on next-generation sequencing. Mol Biol Rep 46(4):4303–4312. https://doi.org/10.1007/s11033-019-04884-7

    Article  CAS  PubMed  Google Scholar 

  44. Ding XP, Mei WL, Huang SZ, Wang H, Zhu JH, Hu W, Ding ZH, Tie WW, Peng SQ, Dai HF (2018) Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon’s blood. PLoS ONE 13(12):e0209258. https://doi.org/10.1371/journal.pone.0209258

    Article  PubMed  PubMed Central  Google Scholar 

  45. An JY, Yin MQ, Zhang Q, Gong DT, Jia XW, Guan YJ, Hu J (2017) Genome survey sequencing of Luffa Cylindrica L. and microsatellite high resolution melting (SSR-HRM) analysis for genetic relationship of Luffa genotypes. Int J Mol Sci 18(9):e1942. https://doi.org/10.3390/ijms18091942

    Article  CAS  PubMed  Google Scholar 

  46. Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110(3):550–560. https://doi.org/10.1007/s00122-004-1871-x

    Article  CAS  PubMed  Google Scholar 

  47. Kumar J, Agrawal V (2017) Analysis of genetic diversity and population genetic structure in Simarouba glauca DC. (an important bio-energy crop) employing ISSR and SRAP markers. Ind Crop Prod 100:198–207. https://doi.org/10.1016/j.indcrop.2017.02.035

    Article  CAS  Google Scholar 

  48. Fu HF, Lv XH, Cheng JY, Li GJ (2018) Analysis of genetic diversity of phenotypic traits and SSR molecular markers in pepper germplasm. J Nucl Agric Sci 32(7):1309–1319. https://doi.org/10.11869/j.issn.100-8551

    Article  Google Scholar 

  49. Chen K, Pachter L (2005) Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol 1(2):106–112. https://doi.org/10.1371/journal.pcbi.0010024

    Article  CAS  PubMed  Google Scholar 

  50. Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14(7):405–409. https://doi.org/10.1186/gb-2013-14-6-405

    Article  PubMed  PubMed Central  Google Scholar 

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Funding

This work was supported by the Key Program of Science and Technology of Shaanxi Province, China (Project No.2013K14-03-01).

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Authors and Affiliations

  1. National Engineering Laboratory for Resource Development of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi’an, 710119, Shaanxi, People’s Republic of China

    Zheng Zhang, Jiawen Zhang, Qing Yang, Bin Li, Wen Zhou & Zhezhi Wang

  2. Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, Shaanxi Normal University, Xi’an, 710119, Shaanxi, People’s Republic of China

    Zheng Zhang, Jiawen Zhang, Qing Yang, Bin Li, Wen Zhou & Zhezhi Wang

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  1. Zheng Zhang
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  2. Jiawen Zhang
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  3. Qing Yang
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  5. Wen Zhou
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Contributions

Conceived and designed the experiments: ZZ. Conducted the experiments: ZZ BL WZ. Analyzed the data: JWZ QY ZZ. Contributed reagents/materials/analysis tools: ZZ. Wrote the paper: JWZ.

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Correspondence to Zhezhi Wang.

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Zhang, Z., Zhang, J., Yang, Q. et al. Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. Mol Biol Rep 48, 241–250 (2021). https://doi.org/10.1007/s11033-020-06042-w

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