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Pakrashi, A.

Publications and source records attributed to Pakrashi, A..

2 recordsLinked to original sources

HAPLODIPOIDY ACCELERATES MITOGENOME EVOLUTION IN INSECTS

Rates of mitogenome evolution differ among animal lineages, variation which has been linked to life history, ecological traits, and potentially to breeding system. Insects are a good model for examining the latter impacts as, although most are diplodiploids (DD), some lineages reproduce by haplodiploidy (HD) or thelytoky. In this study, we ask if breeding system influences patterns of evolution in the mitogenome using the 658 bp barcode region of the cytochrome c oxidase I (COI) gene as a sentinel. Specifically, we ask if the incidence of amino acid substitutions and indels is linked to breeding system. We investigated this matter by examining COI sequences from specimens assigned to 1332 BINs, a species proxy. Belonging to 513 families and 26 orders, these BINs included representatives of roughly half of all insect families. Most are DD, but ten lineages, varying in rank from tribe to order, are HD. Our analysis reveals that HD lineages show higher rates of amino acid substitution than DD. In addition, indels are frequent in HD lineages but are absent in DD taxa with one exception. Among DD, the Strepsiptera is an outlier; its COI shows very rapid amino acid evolution and frequent indels. The accelerated rates of mitogenome evolution in HD lineages suggest that this breeding system facilitates coevolution between the nuclear and mitochondrial genomes.

evolutionary biology↗

Sequencing and characterization of the complete mitochondrial genome of Critically Endangered Black Soft-shell Turtle (Nilssonia nigricans)

The complete mitochondrial genome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was firstly sequenced and annotated. The mitogenome was encoded by 37 genes and a major non-coding Control Region (CR). The mitogenome was A+T biased (62.16%) and spread with six overlapping and 19 intergenic spacer regions. The initiation codons were exceptionally changed as ATA, ATT, and ATC in three Protein-coding genes (PCGs) and a single base (A, T, and C) incomplete termination codons in nine PCGs. The Relative synonymous codon usage (RSCU) value was consistent among all the studied species; exception with significant reduction of Serine (S) frequency in N. nigricans, N. formosa, and R. swinhoei. The secondary structure of N. nigricans showed a lack of conventional dihydrouridine (DHU) arm in trnS (GCT), as well as formed a small loop structure in the acceptor stem of both trnR (TCG) and trnH (GTG). The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in CR. Further, the average Ka/Ks values of 13 PCGs were indicating a strong natural selection in the studied Trionychidae species. The constructed Maximum Likelihood (ML) phylogeny by PCGs shows cohesive clustering of N. nigricans with N. formosa. The resulted phylogeny illustrated the similar topology by all studied species from different taxonomic ranks and supported the previous taxonomic classification. Moreover, further taxon sampling from different taxonomic hierarchy, and their mitogenomics study is vital to reconcile the Testudines phylogeny and assure their evolutionary relationship.

genomics↗