The sequence and de novo assembly of the giant panda genome

Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.

Mechanism for Giycinebetaine to Improve Plant Salt Resistance and Its Research Advances in Genetic Engineering

The paper systematically discusses the mechanism for glycinebetaine to improve plant salt resistance and its research advances in genetic engineering at home and abroad as well as summarizing the research progresses about the key enzymes and their genetic engineering in glycinebetaine biosynthesis. It suggests that on the basis of further understanding the mechanism for glycinebetaine to improve plant salt resistance,the transformation of the genes relating to glycinebetaine biosynthesis should be carried out in major crops so that new plant varieties resistant to salt can be obtained.

Assessment of cattle genetic introgression into domestic yak populations using mitochondrial and microsatellite DNA markers

Hybridization between yak Poephagus grunniens and taurine Bos taurus or indicine B. indicus cattle has been widely practiced throughout the yak geographical range, and gene flow is expected to have occurred between these species. To assess the impact of cattle admixture on domestic yak, we examined 1076 domestic yak from 29 populations collected in China, Bhutan, Nepal, India, Pakistan, Kyrgyzstan, Mongolia and Russia using mitochondrial DNA and 17 autosomal microsatellite loci. A cattle diagnostic marker-based analysis reveals cattle-specific mtDNA and/or autosomal microsatellite allele introgression in 127 yak individuals from 22 populations. The mean level of cattle admixture across the populations, calculated using allelic information at 17 autosomal microsatellite loci, remains relatively low (mY(cattle) = 2.66 +/- 0.53% and Q(cattle) = 0.69 +/- 2.58%), although it varies a lot across populations as well as among individuals within population. Although the level of cattle admixture shows a clear geographical structure, with higher levels of admixture in the Qinghai-Tibetan Plateau and Mongolian and Russian regions, and lower levels in the Himalayan and Pamir Plateau region, our results indicate that the level of cattle admixture is not significantly correlated with the altitude across geographical regions as well as within geographical region. Although yak-cattle hybridization is primarily driven to produce F-1 hybrids, our results show that the subsequent gene flow between yak and cattle took place and has affected contemporary genetic make-up of domestic yak. To protect yak genetic integrity, hybridization between yak and cattle should be tightly controlled.

Lack of genetic association between the angiotensin-converting enzyme gene insertion/deletion polymorphism and longevity in a Han Chinese population

Introduction. The insertion/deletion polymorphism of the angiotensin-converting enzyme (ACE) gene has been reported to associate with human longevity. However, little information is available in a Han Chinese longevity Population. Therefore, we investigat

Exploring factors shaping population genetic structure of the freshwater fish Sinocyclocheilus grahami (Teleostei, Cyprinidae)

Phylogeographical analyses on Sinocyclocheilus grahami samples from seven localities within the Lake Dianchi Basin in China were conducted to explore the main factors shaping population structure within this species. Phylogenetic and network analyses reve

Characterization of TRPC2, an Essential Genetic Component of VNS Chemoreception, Provides Insights into the Evolution of Pheromonal Olfaction in Secondary-Adapted Marine Mammals

Pheromones are chemical cues released and sensed by individuals of the same species, which are of major importance in regulating reproductive and social behaviors of mammals. Generally, they are detected by the vomeronasal system (VNS). Here, we first investigated and compared an essential genetic component of vomeronasal chemoreception, that is, TRPC2 gene, of four marine mammals varying the degree of aquatic specialization and related terrestrial species in order to provide insights into the evolution of pheromonal olfaction in the mammalian transition from land to water. Our results based on sequence characterizations and evolutionary analyses, for the first time, show the evidence for the ancestral impairment of vomeronasal pheromone signal transduction pathway in fully aquatic cetaceans, supporting a reduced or absent dependence on olfaction as a result of the complete adaptation to the marine habitat, whereas the amphibious California sea lion was found to have a putatively functional TRPC2 gene, which is still under strong selective pressures, reflecting the reliance of terrestrial environment on chemical recognition among the semiadapted marine mammals. Interestingly, our study found that, unlike that of the California sea lion, TRPC2 genes of the harbor seal and the river otter, both of which are also semiaquatic, are pseudogenes. Our data suggest that other unknown selective pressures or sensory modalities might have promoted the independent absence of a functional VNS in these two species. In this respect, the evolution of pheromonal olfaction in marine mammals appears to be more complex and confusing than has been previously thought. Our study makes a useful contribution to the current understanding of the evolution of pheromone perception of mammals in response to selective pressures from an aquatic environment.

Genetic diversity of the black crested gibbon (Nomascus concolor) from the Wuliang Mountains of Yunnan, China: preliminary results.

The authors thank Peng Shi, Scott Groom, and two anonymous reviewers for helpful comments. This work was supported by grants from the National Basic Research Program of China (973 Program, 2007CB411600), National Natural Science Foundation of China, and Bureau of Science and Technology of Yunnan Province (to Y.-P.Z.).

Matrilineal Components and Genetic Relationship of Silkies from China and Japan

Silkie is a famous black-bone chicken breed with beautiful silky feather. The unique medical property of this chicken was recorded in Chinese traditional medicine dictionary about 700 years ago. In this study, we analyzed the mtDNA D-loop sequence variation of 26 Bairong Silkies from Fujian Province, China, together with 100 reported Silkie mtDNAs from China and Japan, and studied their matrilineal components and genetic relationship. A total of 21 haplotypes were detected, which could be assigned to six haplogroups (A-E, G). Among them, haplogroups D and G were exclusively presented in Japanese Silkies and Chinese Silkies, respectively. Chinese Silkies had higher frequency of lineages belonging to haplogroups A, B, and E, and lower frequency of haplogroup C than Japanese Silkies. For the four Chinese Silkie populations, most of samples of Taihe, Chengdu, and Hubei Silkies were grouped in haplogroups A, B, and C, whereas most of Bairong Silkies were grouped in haplogroup E. Five haplotypes were shared by Japanese and Chinese Silkies. The genetic diversity of each Silkie population varied, but the overall diversity of Chinese Silkies was similar to that of Japanese Silkies. Taken together, our results confirmed the genetic connection between Chinese and Japanese Silkies, but also clearly showed that the matrilineal genetic structures of Chinese and Japanese Silkies had some differences.

Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene

The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the similar to 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst = 0.70, P < 0.00001; Nm = 0.21) and Minjiang River (Fst = 0.73, P < 0.00001; Nm = 0.18) groups, while low Fst value (Fst = 0.018, P > 0.05) and high rate of migration (Nm = 28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (<= 0.12) and high Nm values (>3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst >= 0.59; Nm < 1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage. (C) 2009 Published by Elsevier B.V.

Genetic Diversity of the Plankton Community and Its Relation to Taxonomic Composition and Environmental Factors in Lake Xiliang

Genetic diversity of the plankton community in Lake Xiliang was depicted by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting. Seventy-seven bands (33 of 16S rDNA and 44 of 18S rDNA) were detected, sixty-two planktonic taxa were identified in six sample stations in November 2007. The most common taxa were Ceratium hirundinella, Bdelloidea, Keratella cochlearis, Polyarthra trigla, and copepod nauplii. Based on environmental factors, taxonomic composition, and PCR-DGGE fingerprinting, unweighted pair-group method using arithmetic averages clustering and principal components analysis were used to analyze habitat similarities. There was distinct spatial heterogeneity in Lake Xiliang, and the genetic diversity of the plankton community was closely related to taxonomic composition and environmental factors.

Increasing the genetic uniformity of bighead carp [Aristichthys nobilis (Richardson)] by means of spontaneous diploidization of gynogenetically activated eggs

Three groups of gynogenetic diploid bighead carp were successfully obtained by means of artificial gynogenesis. The activation rates of gynogenesis varied from 75.9% to 98.8%, and the frequency of spontaneous diploidization was around 0.4%. Over 2000 normally gynogenetic diploid fry were obtained in three gynogenetic groups. The haploid karyotype consisted of nine metacentric, 12 submetacentric, three subtelocentric chromosomes and 45 arms. The chromosome number was 48 from gynogenetic diploid. The results showed that the genetic material of offspring was maternal. The aneuploid hybrid embryos of bighead carp and Xingguo red common carp with chromosome numbers ranging from 28 to 73 did not survive post hatch, likely the result of incompatibility between the nucleus and the cytoplasm of two parents. Sixty RAPD primers from three groups were used for total DNA amplification of gynogenetic offspring, maternal and 'paternal' fish. A total of 451 bands were amplified from three kinds of samples above. From maternal bighead carp, 256 bands were amplified; however, there were 251 shared bands between maternal and gynogenetic bighead carp. From artificial gynogenetic offspring, two 'paternal' DNA segments without an expression function were found. An UPGMA tree showed that gynogenetic offspring were closely clustered and the genetic identity among them was very high (0.956).