Complete mitochondrial genome of the Amur hedgehog Erinaceus amurensis (Erinaceidae) and higher phylogeny of the family Erinaceidae

Abstract

ABSTRACT. We sequenced and characterized the complete mitogenome (KX964606) of the Amur hedgehog Erinaceus amurensis to provide more data for comparative mitogenomics of the genus Erinaceus (Erinaceidae). The mitogenome of E. amurensis is a circular molecule 16,941 bp long, consisting of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of E. amurensis is AT-biased, with a nucleotide composition of 33.9% A, 21.1% C, 32.6% T, and 12.4% G. The mitogenomes of E. amurensis and the closely related hedgehog species E. europaeus, excluding the control region (66.7%), share over 90% sequence similarity. According to the inter-generic relationship based on six mitogenomes described from five genera of Erinaceidae, the subfamilies Erinaceinae and Galericinae are strongly supported as monophyletic groups, with each genus well placed within its own subfamily. Within the subfamily Erinaceinae, E. amurensis is a sister species to E. europaeus, and the relationship between Hemiechinus and Erinaceus is strongly supported. Within the subfamily Galericinae, the clade of Hylomys + Neotetracus was sister to that of Echinosorex, with clades supported by high values. Our findings will help to understand the codon usage pattern and molecular evolution of E. amurensis, and provide insight into intergeneric relationships within the family Erinaceidae. In future studies, the inclusion of mitogenomes from other genera would greatly enhance our understanding of higher phylogeny within the Erinaceidae.

Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia)

“…The most abundant start and stop codons were ATG and TAA, respectively, a finding that agrees with previous work on other mammal mitogenomes [ 30 , 31 , 35 , 37 , 65 , 66 ]. Incomplete stop codons (T-- or TA-), like those used in three PCGs ( Nd1 , Cox3 , and Nd4 ), are commonly observed in metazoan mitogenomes.…”

“…Accordingly, leucine (15.1–15.5%), isoleucine (8.9–9.7%), threonine (8.2–8.3%), serine (7.5–7.7%), alanine (6.8–6.9%), phenylalanine (6.2–6.3%), methionine (5.7–6.0%) and glycine (5.6–5.7%) are the most common amino acids found in the mitochondria protein sequences, comprising approximately 65% of the coded amino acids. The high proportion of A+T in PCGs appears to be a shared feature in mammal species [ 35 , 66 ]. For any amino acid, the relative synonymous codon usage value (RSCU) is equivalent to the number of times that a codon appears in a gene in relation to the number of expected occurrences under an assumption of equal codon usage.…”

The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle (Bos taurus), and Its Phylogenetic Analysis

“…Indices of codon usage bias show differences in the occurrence of codon usage, indicating genomic evolutionary patterns [27]. Start (ATG) and stop (TAA) codons were the most abundant in the PCC mitogenome, which is in agreement with the mitochondrial genome of other mammals [26,28,29]. Incomplete stop codon presence is commonly found in mitogenomes of other vertebrates [30][31][32], which might be further completed by the posttranscriptional poly-adenylation of the 3 end of the mRNA [33,34].…”

The Complete Mitochondrial Genome of a Neglected Breed, the Peruvian Creole Cattle (<em>Bos taurus</em>), and Its Phylogenetic Analysis

“…Indices of codon usage bias are used to measure differences in the occurrence of codon usage that indicate the evolutionary patterns of their genome [39]. Start and stop codons ATG and TAA, respectively were the most abundant in PCC mitogenome, which is in agreement with the mitochondrial genome of other mammals [38,40,41]. The presence of incomplete stop codons is a common phenomenon found in mitogenomes of other vertebrates [42][43][44].…”