The white shark (Carcharodon carcharias; Chondrichthyes, Elasmobranchii) is one of the most publicly recognized marine animals. Here we report the genome sequence of the white shark and comparative evolutionary genomic analyses to the chondrichthyans, whale shark (Elasmobranchii) and elephant shark (Holocephali), as well as various vertebrates. The 4.63-Gbp white shark genome contains 24,520 predicted genes, and has a repeat content of 58.5%. We provide evidence for a history of positive selection and gene-content enrichments regarding important genome stability-related genes and functional categories, particularly so for the two elasmobranchs. We hypothesize that the molecular adaptive emphasis on genome stability in white and whale sharks may reflect the combined selective pressure of large genome sizes, high repeat content, high long-interspersed element retrotransposon representation, large body size, and long lifespans, represented across these two species. Molecular adaptation for wound healing was also evident, with positive selection in key genes involved in the wound-healing process, as well as Gene Ontology enrichments in fundamental wound-healing pathways. Sharks, particularly apex predators such as the white shark, are believed to have an acute sense of smell. However, we found very few olfactory receptor genes, very few trace amine-associated receptors, and extremely low numbers of G protein-coupled receptors. We did however, identify 13 copies of vomeronasal type 2 (V2R) genes in white shark and 10 in whale shark; this, combined with the over 30 V2Rs reported previously for elephant shark, suggests this gene family may underlie the keen odorant reception of chondrichthyans.

The Bornean elephant population in Sabah, with only 2,000 individuals, is currently mainly restricted to a limited number of forest reserves. The main threats to the species" survival are population fragmentation and isolation of the existing herds. To support and help monitor future conservation and management measures, we assessed the genetic diversity and population structure of Bornean elephants using mitochondrial DNA, microsatellites and single nucleotide polymorphisms. Our results confirmed a previously reported lack of mitochondrial control region diversity, characterized by a single widespread haplotype. However, we found low but significant degree of genetic differentiation among populations and marked variation in genetic diversity with the other two types of markers among Bornean elephants. Microsatellite data showed that Bornean elephants from the Lower Kinabatangan and North Kinabatangan ranges are differentiated and perhaps isolated from the main elephant populations located in the Central Forest and Tabin Wildlife Reserve. The pairwise F ST values between these sites ranged from 0.08 to 0.14 (p < 0.001). Data from these markers also indicate that the Bornean elephant populations from Lower Kinabatangan Wildlife Sanctuary and North Kinabatangan (Deramakot Forest Reserve) possess higher levels of genetic variation compared to the elephant populations from other areas. Our results suggest that (i) Bornean elephants probably derive from a very small female population, (ii) they rarely disperse across current human-dominated landscapes that separate forest fragments, and (iii) forest fragments are predominantly comprised of populations that are already undergoing genetic drift. To maintain the current levels of genetic diversity in fragmented habitats, conservation of the Bornean elephants should aim at securing connectivity between spatially distinct populations. Study sites and samplingElephants in Sabah are distributed in five main ranges: i) Lower Kinabatangan, ii) North Kinabatangan (Deramakot, Tangkulap and Segaliud Forest Reserves), iii) Central Forest (Ulu Segama, Malua, Kuamut, Gunung Rara, and Kalabakan Forest Reserves, Danum Valley and Maliau Basin Conservation Areas), iv) Tabin Wildlife Reserve, and v) Ulu Kalumpang (Alfred et al., 2010; Elephant Action Plan, Sabah Wildlife Department, 2012-2016. All ranges (but Ulu Kalumpang, due to its inaccessibility) were covered and systematically searched for elephant feces between October 2005 and November 2007 (Figure 1). Samples were mainly collected along logging roads where elephants consume grass and travel. The same procedure was conducted for three ranges (Central Sabah, Tabin and North Kinabatangan). For the Lower Kinabatangan population, samples were collected along the main river, in riparian feeding areas where individuals were encountered, allowing collection of fresh samples. Samples were collected during field expeditions of 5-7 days, giving a short time period during which samples were collected from every location. Fresh elephant du...

A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering >50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni. Using a nonredundant set of predicted proteins, >50% (16,823) of sequences showed significant homology to known proteins and ∼38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a genomic foundation supporting S. thompsoni as a model species for further examination of the exceptional rates and patterns of genomic evolution shown by urochordates. Additionally, genomic data will allow for the development of molecular indicators of key life history events and processes and afford new understandings and predictions of impacts of climate change on this key species of Antarctic pelagic ecosystems.

AbstractsBackgroundPigs with SCID can be a useful model in regenerative medicine, xenotransplantation, and cancer cell transplantation studies. Utilizing genome editing technologies such as CRISPR/Cas9 system allows us to generate genetically engineered pigs at a higher efficiency. In this study, we report generation and phenotypic characterization of IL2RG knockout female pigs produced through combination of CRISPR/Cas9 system and SCNT. As expected, pigs lacking IL2RG presented SCID phenotype.MethodsFirst, specific CRISPR/Cas9 systems targeting IL2RG were introduced into developing pig embryos then the embryos were transferred into surrogates. A total of six fetuses were obtained from the embryo transfer and fetal fibroblast cell lines were established. Then IL2RG knockout female cells carrying biallelic genetic modification were used as donor cells for SCNT, followed by embryo transfer.ResultsThree live cloned female piglets carrying biallelic mutations in IL2RG were produced. All cloned piglets completely lacked thymus and they had a significantly reduced level of mature T, B and NK cells in their blood and spleen.ConclusionsHere, we generated IL2RG knockout female pigs showing phenotypic characterization of SCID. This IL2RG knockout female pigs will be a promising model for biomedical and translational research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12958-016-0206-5) contains supplementary material, which is available to authorized users.

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events.

BackgroundAn enduring question surrounding sex chromosome evolution is whether effective hemizygosity in the heterogametic sex leads inevitably to dosage compensation of sex-linked genes, and whether this compensation has been observed in a variety of organisms. Incongruence in the conclusions reached in some recent reports has been attributed to different high-throughput approaches to transcriptome analysis. However, recent reports each utilizing RNA-seq to gauge X-linked gene expression relative to autosomal gene expression also arrived at diametrically opposed conclusions regarding X chromosome dosage compensation in mammals.ResultsHere we analyze RNA-seq data from X-monosomic female human and mouse tissues, which are uncomplicated by genes that escape X-inactivation, as well as published RNA-seq data to describe relative X expression (RXE). We find that the determination of RXE is highly dependent upon a variety of computational, statistical and biological assumptions underlying RNA-seq analysis. Parameters implemented in short-read mapping programs, choice of reference genome annotation, expression data distribution, tissue source for RNA and RNA-seq library construction method have profound effects on comparing expression levels across chromosomes.ConclusionsOur analysis shows that the high number of paralogous gene families on the mammalian X chromosome relative to autosomes contributes to the ambiguity in RXE calculations, RNA-seq analysis that takes into account that single- and multi-copy genes are compensated differently supports the conclusion that, in many somatic tissues, the mammalian X is up-regulated compared to the autosomes.

No abstract

Aim To elucidate the historical phylogeography of the dusky pipefish (Syngnathus floridae) in the North American Atlantic and Gulf of Mexico ocean basins.Location Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States.Methods A 394-bp fragment of the mitochondrial cytochrome b gene and a 235-bp fragment of the mitochondrial control region were analysed from individuals from 10 locations. Phylogenetic reconstruction, haplotype network, mismatch distributions and analysis of molecular variance were used to infer population structure between ocean basins and time from population expansion within ocean basins. Six microsatellite loci were also analysed to estimate population structure and gene flow among five populations using genetic distance methods (F ST , Nei's genetic distance), isolation by distance (Mantel's test), coalescent-based estimates of genetic diversity and migration patterns, Bayesian cluster analysis and bottleneck simulations.Results Mitochondrial analyses revealed significant structuring between ocean basins in both cytochrome b (F ST = 0.361, P < 0.0001; F CT = 0.312, P < 0.02) and control region (F ST = 0.166, P < 0.0001; F CT = 0.128, P < 0.03) sequences. However, phylogenetic reconstructions failed to show reciprocal monophyly in populations between ocean basins. Microsatellite analyses revealed significant population substructuring between all locations sampled except for the two locations that were in closest proximity to each other (global F ST value = 0.026). Bayesian analysis of microsatellite data also revealed significant population structuring between ocean basins. Coalescent-based analyses of microsatellite data revealed low migration rates among all sites. Mismatch distribution analysis of mitochondrial loci supports a sudden population expansion in both ocean basins in the late Pleistocene, with the expansion of Atlantic populations occurring more recently.Main conclusions Present-day populations of S. floridae do not bear the mitochondrial DNA signature of the strong phylogenetic discontinuity between the Atlantic and Gulf coasts of North America commonly observed in other species. Rather, our results suggest that Atlantic and Gulf of Mexico populations of S. floridae are closely related but nevertheless exhibit local and regional population structure. We conclude that the present-day phylogeographic pattern is the result of a recent population expansion into the Atlantic in the late Pleistocene, and that life-history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.