http://www.gigadb.org en-us Fri, 14 Jul 2017 10:26:14 +0000 http://gigadb.org/dataset/100318 Thu, 13 Jul 2017 00:00:00 +0000 Herein, we present a novel and efficient computational tool named Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high depth whole-genome sequencing (WGS) data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean 68× depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats (LTR). Among the 9342 RIPs, 4828 were located in gene regions and five were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but approximately neutral selection for Alu elements based on the frequency spectrum of RIPs.
SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population and should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof-of-concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms (SNPs).
]]> http://gigadb.org/dataset/100302 Wed, 12 Jul 2017 00:00:00 +0000 http://gigadb.org/dataset/100326 Tue, 11 Jul 2017 00:00:00 +0000 http://gigadb.org/dataset/100240 Tue, 11 Jul 2017 00:00:00 +0000 http://gigadb.org/dataset/100321 Fri, 07 Jul 2017 00:00:00 +0000 The draft genome of P. charcoti is 709 Mb in size. The N50 contig length is 6,145 bp and its N50 scaffold length 178,362 kb. The genome of P. charcoti is predicted to contain 32,712 genes, 18,455 of which have been assigned preliminary functions. A total of 8,951 orthologous groups common to seven species fish were identified, while 333 genes were identified in P. charcoti only; 2,519 orthologous group were also identified in both P. charcoti and N. coriiceps, another Antarctic fish. Four gene ontology (GO) terms were statistically overrepresented among the 333 genes unique to P. charcoti, according to GO enrichment analysis.
The draft P. charcoti genome will broaden our understanding of the evolution of Antarctic fish in their extreme environment. It will provide a basis for further investigating the unusual characteristics of Antarctic fishes. ]]> http://gigadb.org/dataset/100320 Thu, 06 Jul 2017 00:00:00 +0000 We constructed a high-quality transcriptome with 34,423 transcripts of which 19,713 (57%) were annotated. Among highly expressed genes (FPKM>100 in one tissue) we found the transition from fasting to digestion was associated with differential expression of 43 genes in the heart, 206 genes in the liver, 114 genes in the stomach, 89 genes in the pancreas and 158 genes in the intestine. We interrogated the function of these genes to test previous hypotheses on the response to feeding. We also used the transcriptome to identify 314 secreted proteins in the gastric fluid of the python.
Digestion was associated with an upregulation of genes related to metabolic processes, and translational changes therefore appears to support the postprandial rise in metabolism. We identify stomach-related proteins from a digesting individual and demonstrate that the sensitivity of modern LC-MS/MS equipment allows the identification of gastric juice proteins that are present during digestion. ]]> http://gigadb.org/dataset/100325 Thu, 06 Jul 2017 00:00:00 +0000 Here we present VaPoR, a highly efficient algorithm that autonomously validates large SV sets using long read sequencing data. We assessed the performance of VaPoR on SVs in both simulated and real genomes and report a high-fidelity rate for overall accuracy across different levels of sequence depths. We show that VaPoR can interrogate a much larger range of SVs while still matching existing methods in terms of false positive validations and providing additional features considering breakpoint precision and predicted genotype. We further show that VaPoR can run quickly and efficiency without requiring a large processing or assembly pipeline.
VaPoR provides a long read based validation approach for genomic SVs that requires relatively low read depth and computing resources and thus will provide utility with targeted or low-pass sequencing coverage for accurate SV assessment. The VaPoR Software is available at: https://github.com/mills-lab/vapor. ]]> http://gigadb.org/dataset/100322 Wed, 05 Jul 2017 00:00:00 +0000 http://gigadb.org/dataset/100314 Wed, 05 Jul 2017 00:00:00 +0000 We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93,000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the database at Taiwan Rice Insertional Mutants Database (http://trim.sinica.edu.tw).
Detailed analyses of phenomics data, T-DNA flanking sequences and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons. ]]> http://gigadb.org/dataset/100288 Tue, 04 Jul 2017 00:00:00 +0000