Comparative mitogenomics of the genus Motacilla (Aves, Passeriformes) and its phylogenetic implications

Abstract

The genus Motacilla belongs to Motacillidae (Passeriformes), where mitochondrial features are poorly understood and phylogeny is controversial. Whole mitochondrial genome (mitogenome) data and large taxon sampling are considered to be ideal strategies to obtain this information. We generated four complete mitogenomes of M. flava, M. cinerea, M. alba and Dendronanthus indicus, and made comparative analyses of Motacilla species combined with mitogenome data from GenBank, and then reconstructed phylogenetic trees based on 37 mitochondrial genes. The mitogenomes of four mitogenome sequences exhibited the same gene order observed in most Passeriformes species. Comparative analyses were performed among all six sampled Motacilla mitogenomes. The complete mitogenomes showed A-skew and C-skew. Most protein-coding genes (PCGs) start with an ATG codon and terminate with a TAA codon. The secondary structures of RNAs were similar among Motacilla and Dendronanthus. All tRNAs except for trnS(agy) could be folded into classic clover-leaf structures. Three domains and several conserved boxes were detected. Phylogenetic analysis of 90 mitogenomes of Passeriformes using maximum likelihood (ML) and Bayesian inference (BI) revealed that Motacilla was a monophyletic group. Among Motacilla species, M. flava and M. tschutschensis showed closer relationships, and M. cinerea was located in a basal position within Motacilla. These data provide important information for better understanding the mitogenomic characteristics and phylogeny of Motacilla.

Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication

“…S3B ). The initiation codon of ATG and the termination codon of TAA are widely present in avian mitogenomic PCGs ( Morinha et al, 2016 ; Hu et al, 2017 ; Yang et al, 2022 ). The incomplete T of nad4 has also been observed in several avian PCGs such as Pyrrhocorax pyrrhocorax and Pyrrhocorax graculus ( Morinha et al, 2016 ).…”

“…Muscle tissue was collected, preserved in 100% ethanol, and stored at −20 °C in the Shaanxi Institute of Zoology, Xi’an, China. Genomic DNA was extracted using a DNeasy kit, and the library reconstruction followed the methodology of previous studies ( Yang et al, 2021 ; Yang et al, 2022 ). The mitogenomes were sequenced using the Illumina HiSeq2000 and Xten platforms, with a paired-end read of 150 bp.…”

“…Most tRNAs were identified using tRNAscan-SE version 1.21 ( Lowe & Eddy, 1997 ), and the remaining tRNAs, rRNAs, and CRs were identified by comparison with other closely related species. The secondary structures of the tRNAs of P. fuscatus were referred to from the results of tRNAscan-SE version 1.21 ( Lowe & Eddy, 1997 ) and other avian mitogenomes ( Yang et al, 2021 ; Yang et al, 2022 ). The conserved elements in CR1 of P. fuscatus were analyzed by referencing previous studies ( Yang et al, 2022 ).…”

“…The secondary structures of the tRNAs of P. fuscatus were referred to from the results of tRNAscan-SE version 1.21 ( Lowe & Eddy, 1997 ) and other avian mitogenomes ( Yang et al, 2021 ; Yang et al, 2022 ). The conserved elements in CR1 of P. fuscatus were analyzed by referencing previous studies ( Yang et al, 2022 ).…”

Taxonomic Status and Phylogenetic Relationship of the Charadriidae Family Based on Complete Mitogenomes

“…PCGs end in complete TAA, TAG, AGG, AGA or AAA codons or with incomplete TA– or T–, which are thought to be completed by posttranscriptional modifications like polyadenylation [ 64 - 67 ]. Only seven genes (Cyt b , ND4L, ND3, ATP6, ATP8, COII and ND6) used the most frequent codon, TAA, as a stop codon.…”