[Advances in mammalian three-dimensional genome by using Hi-C technology approach].

Mammalian genomic DNA in the cell nucleus doesn't exist in linear form but is highly folded and condensed into chromatin with a three-dimensional (3D) structure possessing a specific spatial structure and conformation. Hi-C, the high-throughput chromosome conformation capture technology, was first published in 2009, and it provides an in-depth view of 3D genomics. According to the size of DNA unit, the 3D hierarchical units of mammalian genome can be categorized sequentially as chromosome territory (CT), chromatin compartment A/B, topological associated domain (TAD), and chromatin loop. These hierarchical structural units play vital roles in gene transcription and regulation. In this review, we summarize the 3D hierarchical division of chromosomes, the effects of hierarchical units and the applications of Hi-C technology in development and disease. This review is intended to provide insights for the further study of 3D genomics in mammals.

Analysis of the cytochrome c oxidase subunit 1 (COX1) gene reveals the unique evolution of the giant panda.

As the rate-limiting enzyme of the mitochondrial respiratory chain, cytochrome c oxidase (COX) plays a crucial role in biological metabolism. "Living fossil" giant panda (Ailuropoda melanoleuca) is well-known for its special bamboo diet. In an effort to explore functional variation of COX1 in the energy metabolism behind giant panda's low-energy bamboo diet, we looked at genetic variation of COX1 gene in giant panda, and tested for its selection effect. In 1545 base pairs of the gene from 15 samples, 9 positions were variable and 1 mutation leaded to an amino acid sequence change. COX1 gene produces six haplotypes, nucleotide (pi), haplotype diversity (Hd). In addition, the average number of nucleotide differences (k) is 0.001629±0.001036, 0.8083±0.0694 and 2.517, respectively. Also, dN/dS ratio is significantly below 1. These results indicated that giant panda had a low population genetic diversity, and an obvious purifying selection of the COX1 gene which reduces synthesis of ATP determines giant panda's low-energy bamboo diet. Phylogenetic trees based on the COX1 gene were constructed to demonstrate that giant panda is the sister group of other Ursidae.

The complete mitochondrial genome sequence of Garrulax poecilorhynchus (Aves, Passeriformes, Timaliidae).

The entire mitochondrial genome of Garrulax poecilorhynchus consists of 17 814 bp and containe 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. The nucleotide composition of the mitogenome of G. poecilorhynchus is A = 5342 (29.99%), T = 4314 (24.22%), G = 2480 (13.92%), and C = 5678 (31.87%). The genome has an overall A + T content of 54.21%, which has a similar value among known genus Garrulax mitogenomes. All the tRNA genes display a typical clover-leaf structure. Garrulax poecilorhynchus share the closest relationship with other two species, G. perspicillatus and G. sannio. These data could serve to enrich the resource of genus Garrulax in systematic, population genetic, and evolutionary biological studies.

Evidence of adaptive evolution of alpine pheasants to high-altitude environment from mitogenomic perspective.

Adaptive evolutions to high-altitude adaptation have been intensively studied in mammals. However, considering the additional vertebrate groups, new perception regarding selection challenged by high-altitude stress on mitochondrial genome can be gained. To test this hypothesis, we compiled and analyzed the mitochondrial genomes of 5 alpine pheasants and 12 low-altitude species in Phasianidae. The results that evolutionary rates of ATP6 and ND6 showing significant fluctuation among branches when involved with five alpine pheasants revealed both genes might have implications with adapting to highland environment. The radical physico-chemical property changes identified by the modified MM01 model, including composition (C) and equilibrium constant (ionization of COOH) (Pk') in ATP6 and beta-structure tendencies (Pß), Pk', and long-range non-bonded energy (El) in ND6, suggested that minor overall adjustments in size, protein conformation and relative orientation of reaction interfaces have been optimized to provide the ideal environments for electron transfer, proton translocation and generation of adenosine triphosphate (ATP). Additionally, three unique substitution sites were identified under selection in ND6, which could be potentially important adaptive changes contributing to cellular energy production. Our findings suggested that adaptive evolution may occur in alpine pheasants, which are an important complement to the knowledge of genetic mechanisms against the high-altitude environment in non-mammal animals.

Characteristic of complete mitochondrial genome and phylogenetic relationship of Garrulax sannio (Passeriformes, Timaliidae).

Garrulax sannio (Passeriformes, Timaliidae) was the medium-sized bird, whose plumage color was similar for both sexes. The complete sequence of the mitochondrial DNA genome from G. sannio used the polymerase chain reaction method. The genome (17 840 bp in length) contained 13 protein-coding genes, 2 rRNA (12S and 16S) genes, 22 tRNA genes and 2 control regions (D-loop). The base composition of G. sannio mitogenome A + T percentage was 52.22%. It is slightly higher than G + C 47.78% which was similar with other vertebrates. Through constructed phylogenetic tree, we could identify its taxonomic status. Therefore, mitochondrial genome was a best way to preserve genetic resources of species.

Characterization of the complete mitochondrial genome and phylogenetic relationship of Pomatorhinus ruficollis (Passeriformes, Timaliinae).

In our study, we first report complete mitogenome for P. ruficollis and obtain basic genetic information. The genome of P. ruficollis is 17 009 bp which contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two control regions. Overall bases composition of the complete mitochondrial genome is 29.70%A, 14.47%G, 23.31% T, 32.52%C. Twelve PCGs and 14 tRNA genes are distributed on the H-strand, ND6 and eight tRNA genes are encoded on the L-strand.

Genetic effects of polymorphisms in myogenic regulatory factors on chicken muscle fiber traits.

The myogenic regulatory factors is a family of transcription factors that play a key role in the development of skeletal muscle fibers, which are the main factors to affect the meat taste and texture. In the present study, we performed candidate gene analysis to identify single-nucleotide polymorphisms in the MyoD, Myf5, MyoG, and Mrf4 genes using polymerase chain reaction-single strand conformation polymorphism in 360 Erlang Mountain Chickens from three different housing systems (cage, pen, and free-range). The general linear model procedure was used to estimate the statistical significance of association between combined genotypes and muscle fiber traits of chickens. Two polymorphisms (g.39928301T>G and g.11579368C>T) were detected in the Mrf4 and MyoD gene, respectively. The diameters of thigh and pectoralis muscle fibers were higher in birds with the combined genotypes of GG-TT and TT-CT (p<0.05). Moreover, the interaction between housing system and combined genotypes has no significant effect on the traits of muscle fiber (p>0.05). Our findings suggest that the combined genotypes of TT-CT and GG-TT might be advantageous for muscle fiber traits, and could be the potential genetic markers for breeding program in Erlang Mountain Chickens.

APOBEC2 mRNA and protein is predominantly expressed in skeletal and cardiac muscles of chickens.

Apolipoprotein B mRNA-editing enzyme catalytic subunit 2 (APOBEC2) plays an important role in regulating and maintaining muscle development in mammals. In this study, we evaluated APOBEC2 mRNA abundance and protein expression and the results indicated that APOBEC2 mRNA was most abundant in skeletal and cardiac muscle, with relatively low expression in the gonads, gizzard and subcutaneous fat tissues of chickens. Immunoreactive APOBEC2 was localized to the cell nucleus of developing myocardium and skeletal myofibers. There were significant differences in mRNA and protein abundance among ages, tissues, and between males and females. In conclusion, APOBEC2 was expressed as the greatest in skeletal muscle and cardiac muscle where it localized to the nucleus. Thus, APOBEC2 may play an important role in muscle development in chickens.

Effect of luteinizing hormone/choriogonadotropin receptor (LHCGR) gene on chicken reproductive traits.

Luteinizing hormone/choriogonadotropin receptor (LHCGR) gene, potentially related to reproductive traits in chickens, was genotyped by using the Pooled DNA Sequencing, PCR-SSCP and Directing Sequencing techniques. 306 Erlang Mountain chickens form one line (SD03, a line that has been selected for egg quality from a local chicken breed in Sichuan province, China) were genotyped in this study. The associations between LHCGR polymorphisms and six reproductive traits [body weight at first egg (BWAFE), weight of first egg, age at first egg (AFE), number of eggs at 300 days of age (EN), body weight at 300 days of age and egg weight at 300 days of age (EWTA)] were estimated using the one-way analysis of variance method. Results showed that SNP +G4058A and SNP +T4099G of the LHCGR gene were significantly associated with BWFE and AFE. Birds with the AG genotype for the +G4058A SNP exhibited shorter AFE (P < 0.05) and greater EN than those of the GG and AA genotypes, suggesting a balancing selection (overdominance); the effect of allele C in SNP +C3021T and allele C in SNP +T4490C on EN and AFE is additive and may reflect the influence of positive selection. These alleles have promise as genetic markers for future marker-assisted selection.

Melatonin receptor genes in vertebrates.

Melatonin receptors are members of the G protein-coupled receptor (GPCR) family. Three genes for melatonin receptors have been cloned. The MT1 (or Mel1a or MTNR1A) and MT2 (or Mel1b or MTNR1B) receptor subtypes are present in humans and other mammals, while an additional melatonin receptor subtype, Mel1c (or MTNR1C), has been identified in fish, amphibians and birds. Another melatonin related orphan receptor, GPR50, which does not bind melatonin, is found exclusively in mammals. The hormone melatonin is secreted primarily by the pineal gland, with highest levels occurring during the dark period of a circadian cycle. This hormone acts systemically in numerous organs. In the brain, it is involved in the regulation of various neural and endocrine processes, and it readjusts the circadian pacemaker, the suprachiasmatic nucleus. This article reviews recent studies of gene organization, expression, evolution and mutations of melatonin receptor genes of vertebrates. Gene polymorphisms reveal that numerous mutations are associated with diseases and disorders. The phylogenetic analysis of receptor genes indicates that GPR50 is an outgroup to all other melatonin receptor sequences. GPR50 may have separated from a melatonin receptor ancestor before the split between MTNR1C and the MTNR1A/B ancestor.

Ontogenic expression pattern and genetic polymorphisms of the retinol-binding protein 4 (RBP4) gene in Erlang mountainous chickens.

Retinol-binding protein 4 (RBP4) is the only circulatory transport protein for vitamin A. Based on the essential role of vitamin A in chicken reproduction, we measured RBP4 mRNA abundance in Erlang mountainous chickens. We also identified and analyzed the gene polymorphism and its effect on reproduction traits among 349 chickens. The expression of RBP4 mRNA showed specific developmental changes and striking differences among tissues. The mRNA abundance was greatest (P<0.05) in the liver, intermediate in the ovary, kidney, small intestine, oviduct and heart, and lowest in the hypothalamus and pituitary, as compared to all other tissues (P<0.05). We detected one single nucleotide polymorphism (g.19942455C>G) in intron 2 of the RBP4 gene. Three genotypes (CC, CG and GG) were identified, with a significant effect of genotype on the age at first egg (AFE), first egg weight (FEW), total eggs at 300 days (TE300), highest continuous laying days (HCLD) and average laying interval (ALI). The GG genotype, where chickens display earlier AFE, more TE300, longer HCLD and shorter ALI, would be genetically advantageous and its selection may improve reproduction traits. These results suggested that the RBP4 gene might play an important role in reproduction traits in chickens.

Genetic diversity and population structure in wild Sichuan rhesus macaques.

Because wild rhesus macaque (Macaca mulatta) populations have suffered major declines, there is a growing need to characterize their genetic and population structure in order to protect the genetic integrity of this species. In this study, we genotyped a sample comprising 120 wild rhesus macaques from six sites in Sichuan Province for 30 nuclear microsatellite (STR) loci using an ABI 3130xl genetic analyzer. Bayesian analyses and PCA clearly differentiated monkeys from Heishui from those at other sites. The samples from all six sites exhibited high gene diversity suggesting that the Sichuan wild rhesus macaque populations are not threatened by a lack of genetic diversity. Deviation from Hardy-Weinberg equilibrium was more frequent in the Danba and Heishui populations. This may be due to the more fragmented habitat and less disturbance by humans in this area that foster greater subpopulation structuring than occurs in eastern China. We suggest that this population subdivision is the result of both long-term geographic barriers and human activity.

Phylogenetic analysis of chinese rhesus macaques (Macaca mulatta) based on mitochondrial control region sequences.

Between one and six subspecies of Chinese rhesus macaques (Macaca mulatta) have been proposed based on morphological differences and/or their geographic distribution. In this study, a 489 base pair fragment of the mitochondrial control region was amplified from 230 DNA samples collected from rhesus macaques in the Sichuan province in Western China. The fragment was then sequenced and aligned with 208 sequences from wild rhesus macaques, sampled throughout the species' geographic range in China downloaded from GenBank. Phylogenetic analysis of the 182 unique sequences identified among these samples divided Chinese rhesus macaques into two western haplogroups (haplogroups A and B) and three older eastern haplogroups (haplogroups C, D, and E), whose differentiation probably occurred during the penultimate glacial event. During the warming after the penultimate glacial event, haplogroups A, B, and E rapidly expanded and a relatively young subhaplogroup of haplogroup E, E', limited to Southern China but shared with Vietnamese rhesus macaques, was reintroduced from Indochina during the last glacial event. One haplotype most closely related to subhaplogroup E' probably represents the isolation of Hainan Island, to where it is restricted, from the mainland by the formation of the Qiongzhou Strait approximately 8,500 years ago. The distribution of haplogroups both informs the phylogeographic history of dispersal of Chinese rhesus macaques and has implications for their suitability as animal models in biomedical research.

Using COI gene sequence to barcode two morphologically alike species: the cotton bollworm and the oriental tobacco budworm (Lepidoptera: Noctuidae).

Due to limited morphological difference, the two closely related sister species, the cotton bollworm, Helicoverpa armigera (Hübner) and the oriental tobacco budworm, H. assulta (Guenée) (Lepidoptera: Noctuidae), are very difficult to distinguish, especially at the larvae stage. Recently, DNA sequence has been widely used as a bio-barcode for species identification. In this study, we attempted to distinguish H. armigera and H. assulta using the mitochondrial cytochrome C oxidase subunit I gene (COI) gene sequence as the barcode. We determined a 658 bp segment of the COI gene for 28 individuals of H. armigera, 8 individuals of H. assulta, and 10 individuals of Mamestra brassicae (as the outgroup) in Yunnan Province, southwest of P. R. China, together with one H. assulta and two H. armigera reported sequences from GenBank. Twenty-three haplotypes were identified in all 49 samples. As expected, network analysis of the haplotypes of the three species presented a clustering pattern consistent with the respective species status. Haplotypes of the same species differed from each other by no more than three nucleotide substitutions. However, each haplotype of H. armigera differed from that of H. assulta by at least 22 nucleotide substitutions. Both species differed from M. brassicae by more than 50 nucleotide substitutions. 17 unique diagnostic nucleotides were also used to discriminate the two species. The finding of large COI sequence differences between H. armigera and H. assulta suggested that it could be used to distinguish the two morphologically alike species and be employed for quick species identification during pest control.