Chaochao Yan

Complete mitochondrial genome sequence of Nectogale elegans

Abstract The elegant water shrew (Nectogale elegans) belongs to the family Soricidae, and distributes in northern South Asia, central and southern China and northern Southeast Asia. In this study, the complete mitochondrial genome of N. elegans was sequenced. It was determined to be 17,460 bases, and included 13 protein-coding genes (PCGs), 22 tRNA genes, 2 ribosomal RNA genes and one non-coding region, which is similar to other mammalian mitochondrial genomes. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 heavy-strand concatenated PCGs. Phylogenetic analyses further confirmed that Crocidurinae diverged prior to Soricinae, and Sorex unguiculatus differentiated earlier than N. elegans.

Complete mitogenome of Chinese shrew mole Uropsilus soricipes (Milne-Edwards, 1871) (Mammalia: Talpidae) and genetic structure of the species in the Jiajin Mountains (China)

The complete mitochondrial genome of the Chinese shrew mole, Uropsilus soricipes (Soricomorpha: Talpidae) was determined (GenBank accession no. JQ658979). The mitogenome is 16,575 base pairs and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. Phylogenetic relationship analysis based on 12 concatenated protein-coding genes revealed that Uropsilus occupies a basal position within Talpidae, which is consistent with previous studies. Additionally, low nucleotide diversity (0.0028) and high haplotype diversity (0.936) of U. soricipes in the Jiajin Mountains and the neutrality test statistics (D=−1.59491, p=0.045; Fs=−4.171, p=0.016) suggest that this population experienced a demographic expansion at about 46,600 years ago. The phylogenetic analysis of the combined data (cytochrome b and D-loop) revealed two clades. Divergence of these clades occurred in the middle Pleistocene 0.986 million years ago. Mountains played a substantial role in shaping the geographical populations of this species.

The complete mitochondrial genome sequence of Shrew Gymnure, Neotetracus sinensis

The Shrew Gymnure Neotetracus sinensis belongs to family Erinaceidae, and distributes in China, Myanmar, and northern Vietnam. In this study, the whole mitochondrial genome of N. sinensis was first sequenced and characterized. The genome is 16,982 bases in length. Bayesian inference and maximum likelihood methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirm the subfamily Galericinae diverged prior to the subfamily Erinaceinae, support the species N. sinensis was in distinct genus Neotetracus rather than Hylomys, and N. sinensis diverged later than Echinosorex gymnura.

Complete mitochondrial genome of blood pheasant (Ithaginis cruentus)

The blood pheasant Ithaginis cruentus belongs to the family Phasianidae and distributes in the eastern Himalayas, India, Nepal, Bhutan and China. In this study, the total mitochondrial genome of I. cruentus was firstly determined. The genome is 16,683 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes on the heavy strand. Phylogenetic analyses further confirmed that Ithaginis clearly diverged later than Arborophila, and Arborophila was a basal branch within Phasianidae.

Complete mitochondrial genome of Hainan partridge, Arborophila ardens (Galliformes: Phasianidae).

Abstract The Hainan partridge, Arborophila ardens belongs to family Phasianidae, and distributes only in Hainan, China. In this study, the complete mitochondrial genome of A. ardens was first sequenced and characterized. The genome is 16,727 bases in length. Bayesian inference, maximum likelihood and maximum parsimony methods were used to construct phylogenetic trees based on 12 concatenated protein-coding genes located on the heavy strand. Phylogenetic analyses further confirm the Arborophila placed at the root of Phasianidae. Arborophila ardens show closer relationship with A. rufipectus than A. rufogularis and A. gingica which cluster as sister group to A. ardens and A. rufipectus.

Phylogenetic analysis of the Mustela altaica (Carnivora: Mustelidae) based on complete mitochondrial genome

Abstract The mountain weasel (Mustela altaica) belongs to family Mustelidae, which is the near threatened species in the IUCN Red List. In this study, the complete mitochondrial genome of M. altaica was sequenced and characterized. The genome is 16,521 bases in length (GenBank accession no. KC815122). The nucleotide sequence data of 12 heavy-strand protein-coding genes of M. altaica and other 20 Mustelidae species were used for phylogenetic analyses. Trees constructed by using Bayesian inference, maximum parsimony and maximum likelihood demonstrated that M. altaica was close to Mustela nivalis and they were sister to Mustela putorius and Mustela sibirica.

Complete mitochondrial genome of Gymnodiptychus pachycheilus (Teleostei: Cypriniformes: Cyprinidae)

Abstract The complete mitochondrial DNA genome of Gymnodiptychus pachycheilus was sequenced and characterized. The genome is 16,586 bp in length. As with most teleosts, the mitogenome of G. pachycheilus is structurally conserved, containing two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes and one displacement loop (D-loop) region. The 12 heavy-strand protein-coding genes of G. pachycheilus and other 15 Schizothoracinae species were used for phylogenetic analysis by Bayesian inference and maximum likelihood methods. The topology demonstrated that G. pachycheilus is relatively close to species in genera of Gymnocypris, Schizopygopsis and Oxygymnocypris but differentiated earlier in Schizothoracinae than them.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes.

As the first systematic examination of simple sequence repeats (SSRs) and guanine-cytosine (GC) distribution in intragenic and intergenic regions of ten primates, our study showed that SSRs and GC displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation. Our results suggest that the majority of SSRs are distributed in non-coding regions, such as the introns, TEs, and intergenic regions. In these primates, trinucleotide perfect (P) SSRs were the most abundant repeats type in the 5′UTRs and CDSs, whereas, mononucleotide P-SSRs were the most in the intron, 3′UTRs, TEs, and intergenic regions. The GC-contents varied greatly among different intragenic and intergenic regions: 5′UTRs > CDSs > 3′UTRs > TEs > introns > intergenic regions, and high GC-content was frequently distributed in exon-rich regions. Our results also showed that in the same intragenic and intergenic regions, the distribution of GC-contents were great similarity in the different primates. Tri- and hexanucleotide P-SSRs had the most GC-contents in the 5′UTRs and CDSs, whereas mononucleotide P-SSRs had the least GC-contents in the six genomic regions of these primates. The most frequent motifs for different length varied obviously with the different genomic regions.

A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Complete mitogenome of Intermediate Egret Ardea intermedia (Ciconiiformes: Ardeidae)

Abstract The Intermediate Egret Ardea intermedia belongs to family Ardeidae, and it is widely distributed over east Africa across the Indian subcontinent to Southeast Asia and Australia. In the present study, the total mitochondrial genome of A. intermedia was determined. The genome is 18,578 bases in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and 2 non-coding regions (CR and CRR), with a base composition of A 30.8%, G 14.0%, T 24.3% and C 30.9%. The dn/ds values of ten PCGs (ND1, ND2, ATP8, ATP6, Cox3, ND3, ND4L, ND4, ND5 and ND6) are below 1. Bayesian inference (BI) and maximum likelihood (ML) methods generated similar topologies. Phylogenies showed that Ardea novaehollandiae and A. intermedia should be assign to Egretta and Ardea, respectively. The mitogenomic data of A. intermedia will be useful in the conservation genetics and phylogeny of the species.