Two mitochondrial genomes in Alcedinidae (Ceryle rudis/Halcyon pileata) and the phylogenetic placement of Coraciiformes

Abstract

Coraciiformes comprises 209 species belonging to ten families with significant divergence on external morphologies and life styles. The phylogenetic placement of Coraciiformes was still in debate. Here, we determined the complete mitochondrial genomes (mitogenomes) of Crested Kingfisher (Ceryle rudis) and Black-capped Kingfisher (Halcyon pileata). The mitogenomes were 17,355 bp (C. rudis) and 17,612 bp (H. pileata) in length, and both of them contained 37 genes (two rRNA genes, 22 tRNA genes and 13 protein-coding genes) and one control region. The gene organizations and characters of two mitogenomes were similar with those of other mitogenomes in Coraciiformes, however the sizes and nucleotide composition of control regions in different mitogenomes were significantly different. Phylogenetic trees were constructed with both Bayesian and Maximum Likelihood methods based on mitogenome sequences from 11 families of six orders. The trees based on two different data sets supported the basal position of Psittacidae (Psittaciformes), the closest relationship between Cuculiformes (Cuculidae) and Trogoniformes (Trogonidae), and the close relationship between Coraciiformes and Piciformes. The phylogenetic placement of the clade including Cuculiformes and Trogoniformes has not been resolved in present study, which need further investigations with more molecular markers and species. The mitogenome sequences presented here provided valuable data for further taxonomic studies on Coraciiformes and other related groups.

Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics

“…Atypical pairings of G-U and unmatched base pairs of A-C, A-A, U-U, and U-C are scattered throughout the stems ( Figure S2). These kinds of mismatched pairs or unmatched base pairs have also been found in other vertebrate and invertebrate mitogenomes (Harlid et al, 1998;Slack et al, 2003;Li et al, 2007;Bi et al, 2012;Zou et al, 2015;Sun et al, 2017;Bi et al, 2019;He et al, 2019).…”

“…The PCR products were electrophoresed on 1.5% agarose gels staining with ethidium bromide, and were visualized by ultraviolet transillumination. The purification and sequencing of the PCR products were same with those described in Sun et al (2017).…”

“…Sequence assembly and annotation were performed with DNASTAR package (Lasergene version 5.0; Madison, WI, USA). The boundaries of rRNA genes and protein coding genes (PCGs) were detected by aligning our sequences with other available Coraciiform mitogenomes in GenBank: Ceryle rudis (NC_024280), Halcyon pileata (NC_024198) (Sun et al, 2017), Halcyon coromanda (NC_028177) (Park et al, unpublished data), Todirhamphus sanctus (NC_011712) (Pratt et al, 2009), Aceros waldeni (NC_015085) (Sammler et al, 2011), Bycanistes brevis (NC_015201) (Pacheco et al, 2011), Penelopides panini (HQ834451) (Sammler et al, 2011), Eurystomus orientalis (NC_011716) (Pratt et al, 2009), Merops viridis (NC_034642) (Huang et al, 2017) and Upupa epops (NC_028178) (Park et al, unpublished). Gene annotations were conducted with the MITOS webserver (Bernt et al, 2013) and tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe et al, 2016).…”

“…The program Modeltest version 3.7 (Posada and Crandall, 1998) chose the GTR + I + G model and the GTR+G model as the appropriate substitution model of sequence evolution for the first and second set of data, respectively. The detailed processes for Bayesian tree construction were the same as those reported previously (Sun et al, 2017). We used two independent runs to confirm the convergence of the Bayesian posterior probabilities (BPP) distribution.…”

“…Molecular phylogenetic investigations based on nuclear (Sibley and Ahlquist, 1990;Kemp, 1995;Johansson et al, 2001;Hackett et al, 2008;Jetz et al, 2012;Ödeen and Hästad, 2013;Jarvis et al, 2014;Prum et al, 2015;Reddy et al, 2017) or mitochondrial gene markers (de los Monteros, 2000;Ericson et al, 2006;Pacheco et al, 2011;Mahmood et al, 2014;Sun et al, 2017;Tamashiro et al, 2019) provided powerful evidence on the separated position of "Bucerotes". The separated position of Leptosomatidae was also supported by molecular phylogenetic investigations (Ericson et al, 2006;Hackett et al, 2008).…”