Biology subjects

Chandra, K.

Publications and source records attributed to Chandra, K..

3 recordsLinked to original sources

bioRxiv2018

The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis

The complete mitogenomes in order Thysanoptera is limited to subfamily Thripinae heretofore. In the present study, we sequenced the first mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome was characterized by 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three control regions (CRs). This mitogenome had two overlapping regions of 4 bp and twenty four intergenic spacers accounting for 165 bp. All the tRNA had typical cloverleaf secondary structures, except for trnV and trnS which lacked DHU stem and loop. The mitogenomes of N. samayunkur was highly rearranged with many unique features as compared to other thrips mitogenomes, atp6 and nad1 were terminated with TAG and TGA stop codons respectively; location of trnL2, trnA, trnC, and trnV was rearranged; and the first control region (CR1) was upstream of nad6. The phylogenetic analysis of 13 PCGs implementing maximum likelihood and Bayesian inference showed the clustering of N. samayunkur with Scirtothrips dorsalis supporting the Scirtothrips genus-group and Sericothripinae morphology based relationships. Generation of more mitogenomes from different hierarchical level in the order Thysanoptera is required to understand the gene rearrangements, phylogeny and evolutionary relationships.

genomics↗

bioRxiv2018

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↗

bioRxiv2018

The complete mitochondrial genome of Melon thrips, Thrips palmi (Thripinae) and comparative analysis: A vector for Tospoviruses

The melon thrips, Thrips palmi is a serious pest and vector for plant viruses on a wide range of economically important crops. DNA barcoding evidenced the presence of cryptic diversity in T. palmi and that warrants exhaustive molecular data. Our present study is on decoding the first complete mitochondrial genome of T. palmi (15,333 bp) through NGS technology. The mitogenome contains 37 genes, including 13 PCGs, two rRNAs, 22 tRNAs, and two control regions. The comparative analyses were conducted for gene arrangements, nucleotide composition, codon usage and phylogenetic relationship with other thrips mitogenomes. The nucleotide composition was 78.29% AT, and 21.72% GC with positive AT skewness (0.09) and negative GC skewness (-0.06). The ATN initiation codons were observed in 12 PCGs except cox1 with unique start codon (TTG). The RSCU analysis revealed Phe, Leu, Ile, Tyr, Asn, Lys and Met were the most frequently used amino acids in all PCGs. The codon CGG (Arg) was absent in T. palmi as compared to other thrips mitogenomes. The Ka/Ks ratio ranges from 0.078 in cox1 to 0.913 in atp8. We observed the typical cloverleaf secondary structure in most of the tRNA genes with a few exceptions; absence of DHU stem and loop in trnV and trnS, absence of DHU loop in trnE, lack of T-arm and loop in trnN. The position of trnS1 (between cox3 and CR2) is unique in T. palmi among all the studied thrips mitogenomes. The mitogenome contained 24 intergenic spacer regions and 12 overlapping regions. The CR2 is 63.77% similar to CR1, indicating a possible duplication and translocation in control region. Both the ML and BI phylogenetic trees revealed the close relationships of Thrips with Scirtothrips as compared to Frankliniella. Thus, more mitogenomes on the diverse thrips species is required to understand the in-depth phylogenetic and evolutionary relationships.

genomics↗