Chenling Zhang

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 ofAythya fuligula(Anatidae:Aythya)

Abstract The mitochondrial genome of Aythya ferina (Anatidae: Aythya) is a circular molecule of 16,616 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region (D-loop). Overall base composition of the complete mitochondrial DNA was 29.42% A, 22.19% T, 32.83% C and 15.56% G. All the genes in A. ferina were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

Complete mitochondrial genome of Eumeces elegans (Squamata: Scincidae)

Abstract Eumeces elegans is a kind of blue-tailed lizard in the genus Eumeces, and widely distributed in southern provinces of China. We sequenced and characterized the complete mitochondrial genome of Eumeces elegans. The total length of the complete mitochondrial genome was 17,304 bp with 13 protein-coding genes, 22 tRNAs, two rRNAs and a control regions. The overall base composition of Eumeces elegans was 31.0% A, 15.0% G, 29.8% C, and 24.2% T. ND6 subunit gene and eight tRNA genes were encoded on the L-stand, and other genes were distributed on the H-strand.

Mitochondrial genome of Dinodon rufozonatum (Squamata: Colubridae: Dinodon)

Abstract Dinodon rufozonatum is a species of nocturnal snake in the family Colubridae, which is native to East Asia. In this study, we determined the complete mitochondrial genome of D. rufozonatum. The results showed that the total length of the mitogenome was 17,188 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 2 control regions and 1 stem-loop region. Overall base composition of the complete mitochondrial DNA was A (34.37%), G (12.61%), C (28.24%), and T (24.78%), so the percentage of A and T (59.15%) was slightly higher than G and C. All the genes in D. rufozonatum were distributed on the H-strand, except for the ND6 subunit gene and ten transfer RNA genes which were encoded on the L-strand.

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.

The complete mitochondrial genome of Aythya fuligula (Anatidae: Aythya).

Abstract Aythya fuligula belongs to the genus of Aythya (Anseriformes, Anatidae), which only has 12 species worldwide. The complete mitochondrial genome sequence of A. fuligula was implemented. A circular molecule of 16,616 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNAs and a non-coding AT-rich region. Its gene arrangement patterns were identical to the most other species of Anseriformes.

The complete mitochondrial genome of Eumeces chinensis (Squamata: Scincidae) and implications for Scincidae taxonomy

Abstract Chinese skink (Eumeces chinensis) is a ground-dwelling oviparous sincid lizard, which is widely distributed in the southern Provinces of China, including Taiwan and Hainan. Here, the complete mitochondrial genome of E. chinensis (17 175 bp in length) has been analyzed for building the database. It contains 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (32.1%), G (14.3%), C (28.8%), and T (24.8%), so the percentage of A and T (56.9%) is slightly higher than G and C (43.1%). All the genes in E. chinensis were distributed on the H-strand, except for the ND6 subunit gene and nine tRNA genes which were encoded on the L-strand. Our phylogeny study shows that E. chinensis and P. egregius are the sister group which belongs to the genus, Plestiodon. In addition, we also prove that Lacertidae is sister to the families, Gekkonidae and Scincidae.

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.

A new species of Rana from the Dabie Mountains in eastern China (Anura, Ranidae)

Abstract A new species Rana dabieshanensis sp. n. is described from the Dabie Mountains in Anhui Province, China, based on morphological character differences and molecular analyses. The new species can be distinguished from its congeners by a combination of diagnostic characters. The results of phylogenetic analyses (based on 12s rRNA, 16s rRNA, ND2, Cyt b, RAG1, BDNF and Tyr) and genetic distances (based on Cyt b) indicate that the new species belongs to the Rana longicrus group, and is placed as the sister taxon to R. hanluica.

Mitochondrial genome of Pachytriton feii (Urodela: Salamandridae)

abstract In this paper, the complete mitochondrial genome of Pachytriton feii is sequenced and reported for the first time. In our result, the complete mitochondrial genome of P. feii is 16 293 bp in length. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and 1 non-coding region (D-loop). All the genes in P. feii were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree was reconstructed using the Bayesian analysis method and contained two major clades. Among Pachytriton (P. feii, Pachytriton labiatus, and Pachytriton brevipes), Paramesotriton laoensis make up the first lineage.