Abstract
Tectaria Cav. is the largest genus of Tectariaceae. Species delimitation in the genus is challenging due to morphological convergence. In this study, we have sequenced the complete chloroplast genome of Tectaria coadunata (J.Sm.) C.Chr. and compared it with other plastome sequences of Tectaria for gene composition and structural variations. The plastome size of T. coadunata was 148,333 bp with one Large Single Copy (LSC; 82,508 bp), Small Single Copy (SSC; 18,965 bp), and duplicated inverted repeat (IR; 23,430 bp) region. The plastome of Tectaria exhibited the absence of genes ccsA, rpl32, as well as two tRNAs, trnP-GGG and trnL-UAG. Nevertheless, nuclear encoded copies of all genes were successfully recovered from the transcriptome of T. coadunata. This is the first report of gene deletion from Tectaria plastome. Seven intergenic spacer regions, viz. ycf1-chlN, atpF-atpH, psbM-petN, ndhE-psaC, trnT-trnfM, psbK-psbI, and trnC-trnG, were identified with high nucleotide diversity (Pi) values. These regions can be used as DNA barcodes for species delimitation in Tectaria. Furthermore, peculiar insertions were observed in the IR region. Phylogenetic analysis placed T. coadunata as a sister to T. decurrens.
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Data availability
The plastome sequence of Tectaria coadunata reported in this study has been deposited to NCBI database (https://www.ncbi.nlm.nih.gov/) with accession number OQ928157.
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Acknowledgements
The study was funded by Department of Science and Technology—SERB Vide Grant No. EEQ/2017/000691. HMK is grateful to DST-SERB for funding and project assistantship to SMK. AMD acknowledges Savitribai Phule Pune University for providing Post-Doctoral Fellowship Vide No. SPPU-PDF/ST/BL/2021/0001.
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AMD contributed to conceptualization, formal analysis, methodology, writing—original draft, and all revisions and provided software. SK was involved in DNA extraction. VTB contributed to conceptualization, methodology, formal analysis, writing—original draft and revisions, and supervision and provided software. ABN was involved in supervision. MMS contributed to sample collection and funding acquisition. HMK was involved in conceptualization, sample collection, funding acquisition and writing—revisions.
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40415_2023_979_MOESM1_ESM.tif
Supplementary file 1: a Mauve alignment of Tectaria plastomes; b IRScope analysis of all Tectaria plastomes exhibiting ambiguities in the assembly of five Tectaria plastomes (TIF 20411 kb)
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Supplementary file 2: Nucleotide diversity analysis in three Tectaria plastomes revealed insertions and deletions (TIF 9134 kb)
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Supplementary file 3: Plastome alignment of three Tectaria plastomes using MultiPIP. Levels of sequence similarity are indicated by red (75 ± 100%), green (50 ± 75%), and white (< 50%) (TIF 943 kb)
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Darshetkar, A.M., Khedkar, S.M., Barvkar, V.T. et al. Chloroplast genome sequence of Tectaria coadunata (Tectariaceae), plastome features, mutational hotspots and comparative analysis. Braz. J. Bot 47, 119–132 (2024). https://doi.org/10.1007/s40415-023-00979-5
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DOI: https://doi.org/10.1007/s40415-023-00979-5