Czech J. Genet. Plant Breed., 2023, 59(3):160-168 | DOI: 10.17221/71/2022-CJGPB

Complete chloroplast genome sequence and characteristics analysis of Qingda no.1 alfalfa (Medicago sativa L. cv. Qingda no.1)Original Paper

Yuling Ren1, Yajun Ma2, Xue Li1, Xiaoan Li1, Guozhu Yang3, Ping Li1,4*
1 College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, P.R. China
2 College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, P.R. China
3 Ecological Environment Engineering Research Center, Qinghai University, Xining, Qinghai, P.R. China
4 State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, P.R. China

Medicago sativa is the most widely cultivated forage legume and one of the most economically valuable crops throughout the world. Qingda no.1 (Medicago sativa L. cv. Qingda no.1) is an excellent alfalfa local variety with strong cold, drought and salt resistance in the three rivers source area of Qinghai. In this study, the whole chloroplast (cp) genome of Qingda no.1 was sequenced, assembled and its structure was analysed by the Illumina high-throughput sequencing technology. The results showed that the chloroplast genome of Qingda no.1 exhibits no obvious typical quadripartite structure; the total length of the chloroplast genome is 125 637 bp; the chloroplast genome contained 111 genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with an overall GC content of 38.33%. The relative synonymous codon usage showed that 68.67% of the codons RSCU > 1 in Qingda no.1, with the preference ending with A and T. The simple sequence repeat (SSR) analysis identified 62 SSR loci. The phylogenetic analysis of the cp genome, Qingda no.1 clustered closely with Medicago sativa KU321683 (Medicago sativa L. cv. KU321683). These results are helpful for the further study of the Qingda no.1 adaptation mechanism to high altitude stress environments.

Keywords: chloroplast genome sequencing; Medicago sativa L. cv. Qingda no.1; phylogenetic analysis; Qinghai-Tibet Plateau

Received: September 5, 2022; Accepted: February 6, 2023; Prepublished online: April 14, 2023; Published: June 12, 2023  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Ren Y, Ma Y, Li X, Li X, Yang G, Li P. Complete chloroplast genome sequence and characteristics analysis of Qingda no.1 alfalfa (Medicago sativa L. cv. Qingda no.1). Czech J. Genet. Plant Breed. 2023;59(3):160-168. doi: 10.17221/71/2022-CJGPB.
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Bankevich A., Nurk S., Antipov D., Gurevich A.A., Dvorki M., Kulikov A.S., Lesin V.M. (2012): A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19: 455-477. Go to original source... Go to PubMed...
    2. Beier S., Thiel T., Münch T., Scholz U., Mascher M. (2017): A web server for microsatellite predicition. Bioinformatics, 33: 2583-2585. Go to original source... Go to PubMed...
    3. Do H.D.K., Kim J.S., Kim J.H. (2013): Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. Gene, 530: 229-235. Go to original source... Go to PubMed...
    4. Ebert D., Peakall R.O.D. (2009): Chloroplast simple sequence repeats (cpSSRs) technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Molecular Ecology Resources, 9: 673-690. Go to original source... Go to PubMed...
    5. Hanson G., Coller J. (2018): Codon optimality, bias and usage in translation and mRNA decay. Nature Reviews Molecular Cell Biology, 19: 20-30. Go to original source... Go to PubMed...
    6. Huotari T., Korpelainen H. (2012): Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes. Gene, 508: 96-105. Go to original source... Go to PubMed...
    7. Jansen R.K., Wojciechowski M.F., Wojciechowski, Sanniyasi E., Seung B.L., Henry D. (2008): Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Molecular Phylogenetics and Evolution, 48: 1204-1217. Go to original source... Go to PubMed...
    8. Jiang H., Bi Y.F., Chen L.X., Shan G. (2012): Physiological characteristics of alfalfa under dry-farming condition. Acta Agrestia Sinica, 20: 1077-1080.
    9. Jin S., Daniell H. (2015): The engineered chloroplast genome just got smarter. Trends in Plant Science, 20: 622-640. Go to original source... Go to PubMed...
    10. Katoh K., Standley D. (2013): MAFFT multiple sequence alignment software version 7 improvements in performance and usability. Molecular Biology and Evolution, 30: 772-780. Go to original source... Go to PubMed...
    11. Kumar S., Stecher G., Tamura K. (2016): Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33: 1870-1874. Go to original source... Go to PubMed...
    12. Li Q., Wan J.M. (2005): Development of a local searching software for SSR sites. Hereditas, 27: 808-810.
    13. Li X.A., Yang G.Z., Tian H.N., Yan E., Yin W., Li P., Shang Y.F., Xiao F., Zhang Z.G., Yang F., Zhao H.K., He S.P., Xiong L.L., Yan X.X., Li C.D., Ma R.R., Zhu X.W., Qi X.Q. (2018): Study on physiological adaptation mechanism of Qingda No.1 new alfalfa strain in Shangmei Village around lake. Xining, Qinghai University.
    14. Liu C., Shi L., Zhu Y., Zhu Y.J., Chen H.M., Zhang J.H., Lin X.H., Guan X.J. (2012): CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics, 13: 715. Go to original source... Go to PubMed...
    15. Paul P., Malakar A.K., Chakraborty S. (2018): Codon usage and amino acids usage influence genes expression level. Genetica, 146: 53-63. Go to original source... Go to PubMed...
    16. Plotkin J.B, Kudla G. (2011): Synonymous but not the same: The causes and consequences of codon bias. Nature Reviews Genetics, 12: 32-42. Go to original source... Go to PubMed...
    17. Quax T.E.F., Claassens N.J., Soll D., John V.D.O. (2015): Codon Bias as a means to fine-tune gene expression. Molecular Cell, 59: 149-161. Go to original source... Go to PubMed...
    18. Rao Y.S., Wu G.Z., Wang Z.F., Wang Z.F., Chai X.W., Nie Q.H., Zhang X.Q. (2011): Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Research, 18: 499-512. Go to original source... Go to PubMed...
    19. Rombel I.T., Sykes K.F., Rayner S., Johnston S.A. (2002): A vector for high-throughput gene identification. Gene, 282: 33-41. Go to original source... Go to PubMed...
    20. Sharp P.M., Emery L.R., Zeng K. (2010): Forces that influence the evolution of codon bias. Philosophical Transactions of the Royal Society B, 365: 1203-1212. Go to original source... Go to PubMed...
    21. Sharpl P.M., Li W.H. (1987): The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15: 1281-1295. Go to original source... Go to PubMed...
    22. Sun Z.X., Ao P.X., Bi Y.F., Shi Q.X.,Yu M. (2022): Complete chloroplast genome sequence and characteristics analysis of Medicago sativa 'Deqin'. Acta Agrestia Sinica, 30: 320-328.
    23. Tao X.L., Ma L.C., Zhang Z.S, Liu W.X., Liu Z.P. (2017): Characterization of the complete chloroplast genome of alfalfa (Medicago sativa) (Leguminosae). Gene Reports, 6: 67-73. Go to original source...
    24. Wang X.Y., Chang X.Y., Peng Q.F., Yang G.Z. (2012): Research on development and degeneration of alfalfa in region of Qinghai Lak. Prataculture & Animal Husbandry, 10: 1-5.
    25. Yang G.F, Su K., Zhao Y.R., Song Z.B., SUN J. (2015): Analysis of codon usage in the chloroplast genome of Medicago truncatula. Acta Prataculturae Sinica, 24: 171-179.
    26. Yang G.Z., Zou H., Zhou P., Yang Y.H., Tian H.N., Nan M.J., Su L.P. (2013): Breeding of a new cold resistant alfalfa strain "Qingda No.1" in alpine pastoral area. Xining, Qinghai University.
    27. Yang G.Z., Yang Y.H., Zou H., Yin W., Zhang Z.G., Tian H.N., Li X.A., Li P., He S.P., Xiong L.L., Yan X.X., Yang F., Chen Y.S., Ma R.R., Li C.D., Zhang X.C., Wang Z.L., Tian Y.Z., Cao G.B., Liu X.M., Zhu X.W., Qi X.Q. (2017): Study on propagation and seed production technology of Qingda No.1 new alfalfa strain. Xining, Qinghai University.
    28. Yang J.B., Li D.Z., Li H.T. (2014): Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Molecular Ecology Resources, 14: 1024-1031. Go to original source... Go to PubMed...
    29. Yuan X.L., Li Y.Q., Zhang J.F, Wang Y. (2021): Analysis of codon usage bias in the chloroplast genome of Dalbergia odorifera. Guihaia, 41: 622-630.
    30. Zhao Y., Che W.G., Bi Y.F. (2015): Analysis of APX activity and transcription level in Medicago sativa L. 'Deqin' under heat stress. Molecular Plant Breeding, 13: 1611-1615.

    This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY NC 4.0), which permits non-comercial use, distribution, and reproduction in any medium, provided the original publication is properly cited. No use, distribution or reproduction is permitted which does not comply with these terms.


    Return to the content