RETRACTED ARTICLE: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family

Sarkar, Indrani; Dey, Prateek; Sharma, Sanjeev Kumar; Ray, Swapna Devi; Kochiganti, Venkata Hanumat Sastry; Singh, Renu; Pramod, Padmanabhan; Singh, Ram Pratap

doi:10.1038/s41598-020-72674-4

Cited by 11 publications

(6 citation statements)

References 42 publications

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“…The role of selection in the evolution of mitochondrial DNA (mtDNA) attracted little attention until recently [ 3 , 9 , 23 , 24 ]. Mitochondrial OXPHOS genes have been shown to display evidence of adaptive evolution in, for example, dogs, bats, birds and fishes [ 21 , 22 , 25 , 26 ], and numerous studies have detected signals of positive selection in mitochondrial genes [ 21 – 23 , 27 ], suggesting positive selection plays a strong potential role in adaptation [ 28 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

et al. 2021

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Background In genus Rhinolophus, species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. Results Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes (ND2 and ND6) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6, respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. Conclusions The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis. These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.

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Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

et al. 2021

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“…Leu was the most encoded amino acid (2,170), and TER was the lowest (85). The Relative Synonymous Codon Usage (RSCU) value greater than 1.0 means a codon is used more frequently 32 . The RSCU values for 31 codons exceeded 1 in the C. hirtinoda cp genome, and of these, the third most frequent codon was A/U with 29 (93.55%), and the frequency of start codons AUG and UGG used demonstrated no bias (RSCU = 1).…”

Section: Resultsmentioning

confidence: 99%

The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis

Liu

Zhu

et al. 2022

Sci Rep

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Chimonobambusa hirtinoda, a threatened species, is only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used to obtain the complete chloroplast (cp) genome sequence of C. hirtinoda. The sequence was assembled and analyzed for phylogenetic and evolutionary studies. Additionally, we compared the cp genome of C. hirtinoda with previously published Chimonobambusa species. The cp genome of C. hirtinoda has a total length of 139, 561 bp and 38.90% GC content. This genome included a large single -copy (LSC) region of 83, 166 bp, a small single-copy (SSC) region of 20, 811 bp and a pair of inverted repeats of 21,792 bp each. We discovered 130 genes in the cp genome, including 85 protein-coding genes, 37 tRNA, and 8 rRNA genes. A total of 48 simple sequence repeats (SSRs) were detected. The A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained by measuring the codon usage frequency of amino acids. Furthermore, phylogenetic analysis using complete cp sequences and matK gene revealed a genetic relationship within the Chimonobambusa genus. This study reported the chloroplast genome of the C. hirtinoda.

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“…Of those amino acids encoded by codons, Leu had the highest presence with 2,170 and TER was lowest at 85. A relative synonymous codon usage (RSCU) value greater than 1.0 means a codon is used more frequently 32 . The RSCU values for 31 codons exceeded 1 in the C. hirtinoda cp genome, and of these the third most frequent codon was A/U with 29 (93.55%), and the codons ending in C and G had values of 1 (3.23%) and 1, respectively (3.23%).…”

Section: Resultsmentioning

confidence: 99%

The Complete Chloroplast Genome of Critically Endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and Phylogenetic Analysis

liu

Zhu

et al. 2021

Preprint

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Chimonobambusa hirtinoda is a threatened species and only naturally distributed in Doupeng Mountain, Duyun, Guizhou, China. Next-generation sequencing (NGS) is used obtained the complete chloroplast (cp) genome sequence of C. hirtinoda, and then the sequence was assembled and analyze for phylogenetic and evolutionary. We also analyzed comparing the cp genome among Chimonobambusa species with previously published. The complete cp genome of C. hirtinoda has the total length of 139, 561 bp, 38.90% GC content was detected. A total of 130 genes were founded in the cp genome, including 85 protein coding genes, 37 tRNA genes, 8 rRNA. Some genes are missing and the introns occur lost in the cp genome of C. hirtinoda. A total of 48 simple sequence repeat (SSR) were detected and by measuring the codon usage frequency of amino acids, the A/U preference of the third nucleotide in the cp genome of C. hirtinoda was obtained. Furthermore, phylogenetic analysis using complete cp sequences, matk gene exhibited genetic relationship within the Chimonobambusa genus.

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RETRACTED ARTICLE: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family

Cited by 11 publications

References 42 publications

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats

The complete chloroplast genome of critically endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and phylogenetic analysis

The Complete Chloroplast Genome of Critically Endangered Chimonobambusa hirtinoda (Poaceae: Chimonobambusa) and Phylogenetic Analysis

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