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The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold

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Abstract

Background

An ornamental plant often seen in gardens and farmhouses, Musa basjoo Siebold can also be used as Chinese herbal medicine. Its pseudostem and leaves are diuretic; its root can be decocted together with ginger and licorice to cure gonorrhea and diabetes; the decoct soup of its pseudostem can help relieve heat, and the decoct soup of its dried flower can treat cerebral hemorrhage. There have not been many chloroplast genome studies on M. basjoo Siebold.

Methods and results

We characterized its complete chloroplast genome using Novaseq 6000 sequencing. This paper shows that the length of the chloroplast genome M. basjoo Siebold is 172,322 bp, with 36.45% GC content. M. basjoo Siebold includes a large single-copy region of 90,160 bp, a small single-copy region of 11,668 bp, and a pair of inverted repeats of 35,247 bp. Comparing the genomic structure and sequence data of closely related species, we have revealed the conserved gene order of the IR and LSC/SSC regions, which has provided a very inspiring discovery for future phylogenetic research.

Conclusions

Overall, this study has constructed an evolutionary tree of the genus Musa species with the complete chloroplast genome sequence for the first time. As can be seen, there is no obvious multi-branching in the genus, and M. basjoo Siebold and Musa itinerans are the closest relatives.

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Data availability

The identified long repeat regions [29] are deposited in GenBank (login No. BankIt2410783 Musa_basjoo_Siebold MW376865). The following supplementary files are available online: Table S1: Summary of the plastid genome features of the 10 Musaceae studied; Table S2: Simple sequence repeats (SSRs) in the Musa basjoo Siebold plastid genome; Table S3: Long repeat sequences in the Musa basjoo Siebold plastid genome.

Code availability

Not applicable.

Abbreviations

PCR:

Polymerase chain reaction quantitative

PE:

Paired-end

RSCU:

Relative synonymous codon usage

ML:

Maximum likelihood

LSC:

Large single copy

SSC:

Short single copy

IRs:

Inverted repeats

mRNA:

Messenger RNAs

rRNA:

Ribosomal RNAs

tRNA:

Transfer RNAs

SSRs:

Simple sequence repeats

dS:

Synonymous

dN:

Non Synonymous

ITS:

Internal transcribed spacer region

IRa:

Inverted repeats a

IRb:

Inverted repeats b

JLB:

Junction line between LSC and IRb

JSB:

Junction line between IRb and SSC

JSA:

Junction line between SSC and IRa

Ka/Ks:

The ratio between the rate of synonymous (Ks), and non-synonymous (Ka) substitutions

CBOL:

The Consortium for the barcode of life

GTR:

General time reversible

RAxML:

Random axelerated maximum likelihood

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Funding

The study was supported by the Start-up Foundation of Introducing Talents for Scientific Research, Nanjing Institute of Industry Technology (Grant No. 201050619YK701), and Nanjing Forestry University foundation (Grant No. 163108059).

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Author notes

  1. Fenxiang Liu and Ali Movahedi have contributed equally to this work.

Authors and Affiliations

  1. School of Business and Trade, Nanjing Vocational University of Industry Technology, Nanjing, 210046, China

    Fenxiang Liu, Dezhi Xu, Jigang Xie & Yu Zhang

  2. Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China

    Ali Movahedi

  3. Department of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, 210023, China

    Wenguo Yang

  4. Genepioneer Biotechnologies Inc., Nanjing, 210023, China

    Chuanbei Jiang

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  1. Fenxiang Liu
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Contributions

FL: Conceptualization, software, formal analysis, writing—original draft, visualization, and project administration; AM: Writing—review & editing, visualization, supervision, and funding acquisition; WT: Validation, writing—review & editing, visualization, supervision, and funding acquisition; DX: Review & editing, and data curation; CJ: Review & editing, and data curation; JX: Review & editing, and data curation; YZ: Review &editing, and data curation.

Corresponding authors

Correspondence to Ali Movahedi or Wenguo Yang.

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The authors have no conflict of interest.

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Liu, F., Movahedi, A., Yang, W. et al. The complete chloroplast genome and characteristics analysis of Musa basjoo Siebold. Mol Biol Rep 48, 7113–7125 (2021). https://doi.org/10.1007/s11033-021-06702-5

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