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Cathartidae is a small family of large-bodied carrion-feeding birds, of which the turkey vulture (Cathartes aura, Cathartidae) is the most widespread distributed. To investigate the chemoreception system, detoxification system, and immune system in the turkey vulture, we compared its genome to 14 other avian genomes. Comparative genomics demonstrated the expansion in the chemoreception system, especially the olfactory receptors, while the genes in the detoxification system of the turkey vulture did not show apparent expansion. We identified five positively selected genes associated with the immune system in the turkey vulture, which was likely to strengthen the immune defense against pathogenic invasion. Functional enrichment analysis indicated that many positively selected genes were involved in the regulation of immune system processes, implying important reorganization of the immune system in the turkey vulture. The turkey vulture-specific missense mutations were found in one positively selected gene (BCL6), and all the missense mutations were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to the carrion feeding. Furthermore, we identified four turkey vulture-specific missense mutations in three β-defensin genes of the turkey vulture, which was an indispensable part in the innate immunity (a natural barrier against invasive microbes including bacteria, fungi, and viruses). Our genomic analyses in the turkey vulture provided insights into the genetic signatures of the adaptation to the carrion feeding. [ABSTRACT FROM AUTHOR]

Microsatellites are found in taxonomically different organisms, and such repeats are related with genomic structure, function and certain diseases. To characterize microsatellites for macaques, we searched and compared SSRs with 1-6 bp nucleotide motifs in rhesus, cynomolgus and pigtailed macaque. A total of 1395671, 1284929 and 1266348 perfect SSRs were mined, respectively. The most frequent perfect SSRs were mononucleotide SSRs. The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs. Chromosome size was positively correlated with SSR number and negatively correlated with the relative frequency and density of SSRs. The GC content of chromosome SSRs were negatively correlated with relative frequency of SSRs and GC content of chromosome sequences. The features of microsatellite distribution in assembled genomes of the three species were greatly similar, which revealed that the distributional pattern of microsatellites is probably conservative in genus Macaca. The degenerated number of repeat motifs was found to be different in pentanucleotide and hexanucleotide repeats. Species-specific motifs for each macaque were significantly underrepresented. Overall, SSR frequencies of each chromosome in rhesus macaque were higher than in cynomolgus macaque. The maximum repeat times of mono- to pentanucleotide repeats in cynomolgus macaque was more than other two macaques. These results emphasize the genetic diversity and phylogenetic relationship of genus Macaca species. Our data will be beneficial for comparative genome mapping, understanding the distribution of SSRs and genome structure between these animal models, and provide a foundation for further development and identification of more macaque-specific SSRs. [ABSTRACT FROM AUTHOR]

The giant panda ( Ailuropoda melanoleuca) is one of the most famous flagship species for conservation, and its draft genome has recently been assembled. However, the transcriptome is not yet available. In this study, the blood transcriptomes of three pandas were characterized and about 160 million sequencing reads were generated using Illumina Hi Seq 2000 paired-end sequencing technology. The assembly yielded 92 598 transcripts with an average length of 1626 bp and N50 length of 2842 bp. Based on a sequence similarity search against nonredundant (nr) protein database, a total of 38 522 (41.6%) transcripts were annotated. Of these annotated transcripts, 25 142 and 8272 transcripts were assigned to gene ontology terms and clusters of orthologous group, respectively. A search against the Kyoto Encyclopedia of Genes and Genomes Pathway database ( KEGG) indicated that 9098 (9.83%) transcripts mapped to 324 KEGG pathways, and the best represented functional categories of pathways were signal transduction and immune system. We have also identified 23 460 microsatellites, 43 560 SNPs as well as 21 456 alternative splicing events in the assembly. Additionally, a total of 24 341 complete open reading frames ( ORFs) were detected from the assembly where 1492 ORFs were found to be novel gene loci as these have not been annotated so far in any public database. [ABSTRACT FROM AUTHOR]

The Chevrier's field mouse ( Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities ( h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b ( cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau. [ABSTRACT FROM AUTHOR]

The Gracile shrew mole ( Uropsilus gracilis) belongs to the family Talpidae, which distributes in southwestern China, extending to northern Myanmar. In this study, the complete mitochondrial genome of U. gracilis was sequenced. It was determined to be of 16,533 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of U. gracilis and other 12 insectivores were used for phylogenetic analysis. Phylogenetic trees were constructed by using Bayesian and maximum likelihood methods, which showed that U. gracilis was clustered together with U. soricipes, and Urotrichus should be prior to Galemys. [ABSTRACT FROM AUTHOR]

The Chinese scrub vole ( Neodon irene) belongs to the subfamily Arvicolinae, which is restricted to mountain areas at high altitudes (2800-4000). In this study, we sequenced the complete mitochondrial genome of N. irene. It was determined to be 16,367 bases. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. irene and other 22 rodents were used for phylogenetic analysis. Bayesian inference (BI) and maximum likelihood (ML) were used. Both the BI and ML trees demonstrated that Microtus rossiaemeridionalis and Microtus kikuchii did not cluster together with each other. On the contrary, M. rossiaemeridionalis showed close relationship with N. irene. In the present study, only one sequence from Neodon and two sequences from Microtus were included in the phylogenetic analysis which should contribute to the unusual relationship. Therefore, in order to better understand the phylogenetic relationship within Rodentia, more rodents' complete mitochondrial genomes are required. [ABSTRACT FROM AUTHOR]

Wood mice of the genusApodemusare the most common small rodents in fields and broad-leaf forests in the temperate zone. In this study, we determined the complete mitochondrial genome ofApodemus latronum. It was endemic species to China, which mainly inhabited at the high land of the eastern Tibetan Plateau. The complete mitochondrial genome sequences ofA. latronumwas estimated to be 16,288 bases. Its organization and order were similar to that of typical vertebrate and other rodents' mitochondrial genomes, which consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Most protein-coding genes used ATG as the initiation codon. However, ND1, ND2 and ND5 began with ATA, whereas ND3 initiated with ATT. The termination codon also showed some degree of variation, and three types of stop codons were observed. The mitogenome sequence ofA. latronumcould provide helpful data to study the phylogeny ofApodemus. [ABSTRACT FROM AUTHOR]

The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii , is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100.93 Mb (9.97%) repeat elements, 785 ncRNA, 5,465,549 bp (0.54%) SSR and 15,550 (92%) genes in public databases. Compared to other birds and mammals, the genome evolution analysis showed numerous expanded gene families and positive selected genes involved in high-altitude adaptation, especially related to the adaptation of low temperature and hypoxia. Consequently, this gene data can be used to investigate the molecular evolution of high-altitude adaptation in future bird research. Our first published genome of the genus Lophophorus will be integral for the study of monal population genetic diversity and conservation, genomic evolution and Galliformes species differentiation in the Qinghai-Tibetan Plateau. • The Chinese monal genome assembly was 1.01 Gb with 16,940 genes. • Global climate change in last glaciation period exerts a strong influence on Chinese monal population numbers. • Genome evolution analysis found that the Chinese monal has a large number of genes involved in environmental adaptation. [ABSTRACT FROM AUTHOR]

Two novel mitogenomes of Eozapus setchuanus ( KJ648495 ) and Sicista concolor ( KJ648496 ) were reported and their total lengths were 16,630 bp and 16,493 bp, respectively. Both mitogenomes which were analogous to other rodent mitogenomes, contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Specifically, the ND2 gene of S. concolor has three amino acids lesser than that of two other Dipodidae species ( E. setchuanus and Jaculus jaculus ) due to a premature termination codon in the 3′ end. We detected a tandem repeat cluster of 221 bp and 274 bp in the control region of S. concolor and E. setchuanus , respectively. Along with phylogenetic relationship analysis, we speculated that the tandem repeats in control regions might be common in Dipodinae species. Our phylogenetic analysis using concatenated mitochondrial gene datasets suggested five suborder and 16 family monophyletic groups in 54 rodent taxa sampled and strongly supported a basal position of the squirrel-related clade (PP = 1; BP = 100). Dipodidae had a sister-group relationship with Muroidea, and Sicistinae was in the base of Dipodidae clade. The complete mitochondrial genomes showed high resolution in deep-level phylogenetic relationship reconstructions of Rodentia. [ABSTRACT FROM AUTHOR]