The mitochondrial genome of the Cinnamon Bittern, Ixobrychus cinnamomeus (Pelecaniformes: Ardeidae): sequence, structure and phylogenetic analysis

Abstract

Ixobrychus cinnamomeus is a member of the large wading bird family, known as Ardeidae. In the present study, we determined the complete mitochondrial genome of I. cinnamomeus for use in future phylogenetic analysis. This circular mitochondrial genome is 17,180 bp in length and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one putative control region. Three conserved domains and a minisatellite of 17 nucleotides with 22 tandem repeats were detected at the end of the control region. Phylogenetic relationships were reconstructed using the nucleotide and corresponding amino acid datasets of 12 concatenated protein-coding genes from the mitochondrial genome. Using maximum likelihood, maximum parsimony and Bayesian inference methods, the monophyly of Ciconiidae, Ardeidae and Threskiornithidae were confirmed; however, the monophyly of traditional Ciconiiformes and Pelecaniformes failed to be recovered. Although further studies are recommended to clarify relationships among and within the orders of Ciconiiformes, Pelecaniformes, Suliformes and Phaethontiformes, our results provide preliminary exploratory results that can be useful in the current understanding of avian phylogenetics.

Complete mitochondrial genome of the Chinese Hwamei Garrulax canorus (Aves: Passeriformes): the first representative of the Leiothrichidae family with a duplicated control region

“…The AT and GC skews, which can be calculated as (A-T) / (A+T) or (G-T) / (G+T) (Perna and Kocher, 1995), for the complete mitochondrial genome of G. canorus are 0.11 and -0.38, respectively, showing a strong bias against guanine. This phenomenon has also been reported in other birds (San Mauro et al, 2004;He et al, 2009;Kan et al, 2010a,b;Zhang et al, 2012 Genes encoded on the heavy or light strands are shown outside or inside the circular gene map, respectively. The inner ring displays the GC content.…”

“…Most tRNA genes were identified using tRNAscan-SE 1.21 (Schattner et al, 2005) using the 'cove only' search mode, with the vertebrate mitochondrial genetic code and 'mito/chloroplast' source. A number of tRNA genes not identified using tRNAscan-SE 1.21 were identified by proposed secondary structures and anti-codons (Zhang et al, 2012). The gene map of the complete mitochondrial genome of G. canorus was initially generated by OGDRAW (Lohse et al, 2007) and then modified manually.…”

“…All the tRNA gene sequences have the potential to fold into typical cloverleaf secondary structures (Figure 2). tRNA Cys and tRNA Ser(AGY) , which were not found by the tRNAscan-SE as reported in other species (Kan et al, 2010a;Zhang et al, 2012), were identified by comparing the sequence with other passerine species counterparts. Table 4).…”

“…Table 4). The nucleotide composition of the G. canorus CR is A = 24.0%, T = 29.5%, C = 33.4%, and G = 13.2%, with a distinct bias against G. Based on the distribution of the conserved motifs in other avian CRs (Brown et al, 1986;Saccone et al, 1991;Randi and Lucchini, 1998;Zhang et al, 2012), the CR1 and CR2 of G. canorus can be separated into three domains: ETAS (extended termination-associated sequences) Domain I, Central Conserved Domain II, and CSB (conserved sequence block) Domain III (Figure 3). Domain I consists of parts A and B.…”

“…The superiority of the mitochondrial genome, such as its small size and fast evolutionary rate, has led to it becoming ever more popular in phylogenetic, phylogeography, and evolutionary studies among animals (Ballard and Whitlock, 2004;Chesser et al, 2010;Kan et al, 2010b,c;Zhang et al, 2012). However, no complete mitochondrial sequence has been reported from members of the family Leiothrichidae.…”