Open Access

ARTICLE

Insight into the characteristics of an important evolutionary model bird (Geospiza magnirostris) mitochondrial genome through comparison

ZHENGGANG XU^1,2,3, LIANG WU³, JIAHAO CHEN¹, YUNLIN ZHAO³, CHONGXUAN HAN¹, TIAN HUANG², GUIYAN YANG^1,*

1 Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, 712100, China
2 Engineering Research Center for Internet of Animals, Changsha, 410000, China
3 Key Laboratory of Forestry Remote Sensing Based Big Data & Ecological Security for Hunan Province, Central South University of Forestry and Technology, Changsha, 410004, China

* Corresponding Author: GUIYAN YANG. Email:

BIOCELL 2022, 46(7), 1733-1746. https://doi.org/10.32604/biocell.2022.015784

Received 13 January 2021; Accepted 04 November 2021; Issue published 17 March 2022

Abstract

Darwin’s finches are the most classic case of evolution. Early studies on the evolution of this species were mainly based on morphology. Until now, the mitochondrial genome of Geospiza magnirostris has been sequenced and the study explored the characteristics of the complete genome of G. magnirostris and verified the evolutionary position of it. The 13 PCGs initiated by ATN codons. The stop codons of three PCGs (ND2, COX3 and ND4) were incomplete, with only T- or TA- replacing complete form TAA or TAG. All the tRNA genes expressed a typical cloverleaf secondary structure, except for tRNA^Ser1(AGY), whose dihydrouridine (DHU) arm was lack and instead with a simple loop. In the sequence of the control region of G. magnirostris, we found six simple repeat tandem sequences with a total length of 42 bp. Two characteristic conserved overlapping junction (ATGCTAA) and (CAAGAAAG) were observed as reported for eight selected Passeriformes birds. A special conserved overlapping junction (ATCTTACC) involved in mitochondrial transcription termination was found between tRNA^Tyr and COX1 in G. magnirostris’s control region. Four most frequently used amino acids in G. magnirostris’s PCGs were Leu1 (CUN), Ile, Thr, Ala. The codon usage of G. magnirostris was relatively average, and there was no particular bias. The ratio Ka/Ks results showed that G. magnirostris receives less natural selection pressure. The phylogenetic relationships and cluster analysis of relative codon usage showed that G. magnirostris and Thraupis episcopus clustered in one branch. The phylogenetic position of G. magnirostris was consistent with the traditional taxonomic of Thraupis. The results supported the conclusion that G. magnirostris belongs to the morphological classification of the family Thraupidae.

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