Analysis of the complete mitochondrial genome sequence of <I>Larus brunnicephalus</I> (Aves, Laridae)

Abstract

The complete sequence of mitochondrial genome of Larus brunnicephalus was determined using long PCR and conserved primers walking approaches. The results showed that the entire mitochondrial genome of L. brunnicephalus is 16,769 bp in length, which has been deposited in GenBank with the accession number JX155863. The mitochondrial genomic organization and gene order of L. brunnicephalus were consistent with that of Gallus gallus, which contains 13 protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. Except for COI gene using GTG and ND3 gene with ATT as the initiation codon, all other 11 PCGs of the mtDNA in L. brunnicephalus started with the typical ATG codon. AGG, TAG, TAA, or AGA were used in 11 PCGs as usual termination codons, except for COIII and ND4 genes with incomplete termination codon (T). The secondary structures of 22 tRNAs were predicted and it is found that the tRNASer (AGN) lacks DHU arm and tRNAPhe contains the fourth types of permutation in the TψC arm. It is predicted that the secondary structures of 12S rRNA and 16S rRNA include 4 structural domains with 47 helics and 6 domains with 60 helics, respectively. F-box, E-box, D-box, C-box, B-box, Bird similarity-box, and CSB-boxes (1-3), which were found in the control regions of other bird species were also present in L. brunnicephalus. The sequence in the starting regions of H-strand replication (OH) and the bidirectional light and heavy-strand transcription promoters (LSP/HSP) in the control region were also predicted. Result of phylogeny analysis supports that L. brunnicephalus should be categorized into the Masked gulls species.

Complete mitochondrial genome MK992912 of Great Knot ( Calidris tenuirostris ) is a chimera with DNA from Pacific Golden Plover Pluvialis fulva (Aves: Charadriiformes)

“… 2018 ), Chroicocephalus brunnicephalus JX155863 (Yang et al. 2012 ), Grus grus FJ769849 (Krajewski et al. 2010 ), Pluvialis apricaria MN122928 (unpublished), Pluvialis fulva KX639757 (Ding et al.…”

The mitochondrial genome of the Saunders's gull Chroicocephalus saundersi (Charadriiformes: Laridae) and a higher phylogeny of shorebirds (Charadriiformes)

“…The primers were designed based on sequence-conserved regions, which were identified using multiple alignments of the complete mitogenomes of Chroicocephalus brunnicephalus, Larus dominicanus, Ichthyaetus relictus, Synthliboramphus antiquus, Arenaria interpres, and Haematopus ater, which are available in GenBank (Paton et al, 2002;Yamamoto et al, 2005;Slack et al, 2007;Yang et al, 2012Yang et al, , 2014 (Table 1). PCR amplification using the primer pairs newly designed for this study (Suppl.…”

“…Of these, four mitogenomes were sequenced from species in the suborder Lari (Laridae and Alcidae), with the other two being sequenced from species in the suborders Scolopaci (Scolopacidae) and Charadrii (Haematopodidae) (Paton et al, 2002;Yamamoto et al, 2005;Slack et al, 2007;Yang et al, 2012Yang et al, , 2014.…”

Complete mitochondrial genome ofChroicocephalus brunnicephalusfrom India: phylogeny with other Larids

“…As of now, 47 complete mitochondrial genomes of Charadriiformes birds are available in the GenBank database. Among them, 13 mitogenomes of 11 Laridae species were generated from different geographical regions (Slack et al 2007;Ryu and Hwang 2012;Yang et al 2012Yang et al , 2016Yang et al , 2017Yoon et al 2015;Dong et al 2016;Kim and Park 2016;Anmarkrud and Lifjeld 2017;Skujina et al 2019). The analysis of the complete mitogenomes was also evidenced to characterize various genomic traits within protein-coding genes (PCGs), ribosomal RNA (rRNA), transfer RNA (tRNA), and control region (CR) as well as to detect gene order evolution in birds (Bensch and H€ arlid 2000;Crochet and Desmarais 2000;Ruokonen and Kvist 2002;Pacheco et al 2011).…”