The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Abstract

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.

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“…New and advanced scientific techniques have emerged to solve these riddles. In the last few years, genome sequencing has become more popular to obtain huge information on evolutionary history and revising the clustering pattern of traditional taxonomy 4 . Mitochondrial DNA with some of its inherent properties like small genome size, absence of extensive recombination frequency, simple structure of genome, maternal inheritance along with rapid evolutionary rate are now extensively utilized in taxonomic and phylogenetic studies of vertebrates 5 – 10 .…”

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

“…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 ).…”

“…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 G content in the second and third codons are low, especially, the G content in the third codons are only 3.6% – 6.0% in 13 Coraciiform mitogenomes. The low G content in third codon positions of mitochondrial PCGs is a common feature in mammalian and avian mitogenomes ( Harlid et al , 1998 ; Gibson et al , 2005 ; Zou et al , 2015 ; Gong et al , 2017 ; Sun et al , 2017 ; Bi et al , 2019 ). The variation ranges of nucleotide content in three codon positions are negatively correlated to the selective pressure that they are subjected to ( Zhong et al , 2002 ).…”