Chaochao Hu

Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin

The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.

Mitochondrial genome of the Emberiza pusilla (Emberizidae: Emberiza)

Abstract Emberiza rutila is a passerine bird of eastern Asia which belongs to the genus Emberiza in the bunting family Emberizidae. The complete mitochondrial genome of E. rutila was obtained for the first time in this study. The circular genome (16,803 bp in length) consists of 37 typical animal mitochondrial genes (13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes) and 1 control region. Overall base composition of the complete mitochondrial DNA was 30% A, 22.8% T, 32.8% C and 14.3% G. Except for 8 tRNA genes and ND6 gene, the relative position and orientation of all the genes were identical to those of most vertebrates.

Mitochondrial genome of theEmberiza aureola(Emberizidae:Emberiza)

The Emberiza pusilla is a common bunting with very wide geographical range. Here, the complete mitochondrial genome of E. pusilla (16,790 bp in length) has been analyzed for building the database. The results showed that it consisted of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The base composition of mtDNA was A (29.6%), G (14.8%), C (32.8%), and T (22.9%), so the percentage of A and T (52.5%) was slightly higher than G and C. All the genes in E. pusilla were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes, which were encoded on the L-strand.

Complete mitochondrial genome of the groundhopper Alulatettix yunnanensis (Insecta: Orthoptera: Tetrigoidea).

In this work, we sequenced the first complete mitochondrial genome of Tetrigoidea species, Alulatettix yunnanensis. The circle genome (15,104 bp) consists of 13 protein-coding, 22 transfer RNA, and 2 ribosomal RNA genes, and an A+T-rich region. It has the typical invertebrate mitochondrial gene arrangement.

The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes

The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5’-AAAC-3’) and 7 bp (5’- AAACAAC -3’) repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.

The complete mitochondrial genome of Scolopax rusticola (Charadriiformes: Scolopacidae)

Abstract In this paper, we report the complete mitochondrial genome of Scolopax rusticola (Charadriiformes: Scolopacidae), which is a circular DNA with 16,984 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The overall base composition of the complete mitochondrial DNA is 31.79% A, 25.02% T, 13.34% G and 29.85% C. The control region is 1413 bp in length which located between tRNAPhe and tRNAGlu.

The complete mitochondrial genome of Anas poecilorhyncha (Anatidae: Anas)

Abstract The mitochondrial genome of Anas poecilorhyncha (Anatidae: Anas) is a circular molecule of 16,608 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region (D-loop). Overall base composition of the complete mitochondrial DNA was 29.17% A, 22.21% T, 32.81% C and 15.81% G.

Mitochondrial genome of the Naemorhedus griseus (Bovidae: Naemorhedus).

Abstract Naemorhedus griseus, vulnerable animal, has undergone a significant decline. Here, we analyzed the complete mitochondrial genome (16,554 bp in length) to supplement the database of N. griseus. The complete mtDNA of N. griseus contained 37 genes (13 protein-coding genes, two rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Additionally, a rep-origin (32 bp) exists which located between tRNAAsn and tRNACys.

Complete mitochondrial genome of Trimeresurus albolabris (Squamata: Viperidae: Crotalinae)

Abstract Trimeresurus albolabris is the most widely distributed species in the genus Trimeresurus and mainly in East and South-East Asia. In this study, we first sequenced and characterized the whole mitochondrial genome of T. albolabris. The total length of the complete mitochondrial genome was 17,220 bp with 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 control regions. The overall base composition of T. albolabris was 33.40% A, 27.04% T, 27.28% C, and 12.28% G. Except for ND6 subunit gene and eight tRNA genes which were encoded on the L-stand, all the genes in T. albolabris were distributed on the H-strand.

The complete mitochondrial genome of Vanellus vanellus (Charadriiformes: Charadriidae).

Abstract The northern lapwing, Vanellus vanellus (Charadriiformes: Charadriidae), is commonly found in temperate Eurasia. In this study, the complete mitogenome sequence of V. vanellus has been determined by polymerase chain reaction (PCR) method using 13 primer pairs. It was a circular molecule with 16,795 bp in length which contained 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The composition and gene order are similar to most other vertebrates. There are 28 genes encoded on the H-strand, 9 genes (ND6 subunit and 8 tRNA genes) encoded on the L-strand. The overall base composition of the H-strand is A (31.44%), T (24.03%), G (13.76%), C (30.77%), with a slight A + T bias of 55.47%. This mitogenome sequence of V. vanellus could contribute to a better solution of its phylogenetic position and will contribute to further genetic researches on Charadriidae.