Abstract
Bambusa is an economically and ornamental woody bamboo genus. The complete plastid genome of B. tulda was determined and analyzed in this study. The genome was 139,536 bp in length, including a large single copy region (LSC) of 83,091 bp and a small single copy region (SSC) of 12,893 bp, and two inverted repeat regions (IR) of 21,776 bp. The plastid genome contained 132 genes, which comprised 85 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes.
Keywords:
Bambusa is one of the largest genera of woody bamboos, containing more than 100 species (Yang et al. Citation2010), which is distributed in the tropics and subtropics from southern Asia to the Pacific Rim, and most of them are high economic value and extensive utility. Bambusa tulda is a costly bamboo which is endemic to northeastern region and West Bengal of India. It is a good material for various handicraft works, house building, paper industries, and other equipment for daily life (Singh et al. Citation2010). The present study acquired a complete plastid genome of B. tulda to investigate the plastid genome feature and phylogenetic position; it also provided the genetic material for evolution and breeding study.
The sample was acquired from Cangshan District, Fujian Province of China (26°38′N, 119°27′E), and the voucher specimen deposited at Herbarium of Fujian Agriculture and Forestry University (specimen code HTY008). The total genomic DNA extraction, library constructing, sequencing and data filtering of B. tulda were referenced in Liu et al. (Citation2020). The plastid genome of B. oldhamii (FJ970915) as reference, the paired-end reads were filtered with GetOrganelle pipe-line (Jin et al. Citation2018) to get plastid-like reads, then the filtered reads were assembled using SPAdes version 3.10 (Bankevich et al. Citation2012). The final ‘fastg’ was filtered by the script of GetOrganelle to get pure plastid contigs, and the filtered ‘De Brujin’ graphs were viewed and edited by Bandage (Wick et al. Citation2015). Assembled plastid genome annotation based on comparison with B. oldhamii using GENEIOUS v11.1.5 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. Citation2012). The matrix of 28 representative species of the tribe Bambuseae was aligned using MAFFT v7.307 (Katoh and Standley Citation2013). The phylogenetic tree was constructed using the maximum-likelihood software IQ-TREE (Nguyen et al. Citation2015) based on the complete plastid genomes; and branch supports with the ultrafast bootstrap (Hoang et al. Citation2018). These analyses are performed in the Phylosuite platform (Zhang et al. Citation2020)
The complete B. tulda (GenBank accession MT028547) plastid genome is a quadripartite structure with the length of 139,536 bp, contains a large single copy region (LSC) of 83,091 bp, a small single copy (SSC) region of 12,893 bp, and two inverted repeat (IR) regions of 21,776 bp. The new sequence possesses total 132 genes, including 85 protein-coding genes, eight rRNA genes, and 39 tRNA genes. The overall GC content of the chloroplast genome was 38.9%, whereas the corresponding values of the LSC, SSC, and IR regions are 37.0%, 33.0%, and 44.2%, respectively. The phylogenetic analysis result showed Bumbusa is monophyletic, and B. tulda is sister to B. emeiensis plus B. emeiensis with strong support ().
Figure 1. The Maximum-Likelihood (ML) tree based on the 28 plastid genomes of Bambuseae. Numbers near the nodes mean bootstrap support value.
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References
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