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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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.
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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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DOI: https://doi.org/10.1007/s11033-021-06702-5