Chloroplast genome sequence of Tectaria coadunata (Tectariaceae), plastome features, mutational hotspots and comparative analysis

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.