@Article{biocell.2022.015784,
AUTHOR = {ZHENGGANG XU, LIANG WU, JIAHAO CHEN, YUNLIN ZHAO, CHONGXUAN HAN, TIAN HUANG, GUIYAN YANG},
TITLE = {Insight into the characteristics of an important evolutionary model bird (<i>Geospiza magnirostris</i>) mitochondrial genome through comparison},
JOURNAL = {BIOCELL},
VOLUME = {46},
YEAR = {2022},
NUMBER = {7},
PAGES = {1733--1746},
URL = {http://www.techscience.com/biocell/v46n7/47033},
ISSN = {1667-5746},
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 <i>Geospiza magnirostris</i> has been sequenced and the study explored the characteristics of the complete genome of <i>G. magnirostris</i> and verified the evolutionary position of it. The 13 PCGs initiated by ATN codons. The stop codons of three PCGs (<i>ND2</i>, <i>COX3</i> and <i>ND4</i>) 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<sup>Ser1</sup>(AGY), whose dihydrouridine (DHU) arm was lack and instead with a simple loop. In the sequence of the control region of <i>G. magnirostris</i>, 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<sup>Tyr</sup> and <i>COX1</i> in <i>G. magnirostris</i>’s control region. Four most frequently used amino acids in <i>G. magnirostris</i>’s PCGs were Leu1 (CUN), Ile, Thr, Ala. The codon usage of <i>G. magnirostris</i> was relatively average, and there was no particular bias. The ratio Ka/Ks results showed that <i>G. magnirostris</i> receives less natural selection pressure. The phylogenetic relationships and cluster analysis of relative codon usage showed that <i>G. magnirostris</i> and <i>Thraupis episcopus</i> clustered in one branch. The phylogenetic position of <i>G. magnirostris</i> was consistent with the traditional taxonomic of <i>Thraupis</i>. The results supported the conclusion that <i>G. magnirostris</i> belongs to the morphological classification of the family Thraupidae.},
DOI = {10.32604/biocell.2022.015784}
}