De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Review of management and monitoring of two crop shrimp production of Indian white shrimp Fenneropenaeus indicus in intensive culture system in Guatr Shrimp Farm, Sistan & Baloochestan Province

In line with the implementation of two Crop shrimp culture in year in Gwater shrimp Farming Site credits UNDP aims to increase production of crops per year, reducing the days of culture in the second crop using the nursery pond, control feed conversion ratio (FCR) and production management, Farming of Indian white Shrimp P.indicus in 4 private farm was done in 2008. Surveillance and monitoring of these farms, the possible obstacles to the harmful effects of management strengths and weaknesses and develop in the future was done in corporation of Offshore Fisheries Research Center of Chabahar and fisheries of Sistan and Balouchestan. First crop was successful, but the shrimp of Nursery pond and second crop due to the occurrence of white spot disease (WSSV) disease and casualties were died and did not actually do the work. The average minimum and maximum feed conversion in Culture period 1.46 and 1.96 respectively, in C2 _31 and C2 _ 14 farms were observed. Maximum production was 41,376 kg in farm C2 _31. The rainfall on 14 August severe flooding and water supplying cussed suddenly fall down of Inland channel water salinity at day 16-20 the August to 4-5 PPT and the PH go up to 8.8-9. After 2 days the white spot disease in South of site was confirmed and was transferred immediately to the north of site. (The pilots farm) The important thing was that the farm under two crop system as a last resort so that all First crop harvest but shrimp in Nursery pond were infected and with veterinary supervision of all infected ponds were then killed. The results showed that shrimp farming can be done in two periods in year with a predetermined .In this study the only factor that could have adverse effects on the project was Feed supply problems during the growing period and the consequences that it caused low average body weight and final harvested Shrimp resulted to delay in daily growth

Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ~30× theoretical coverage, were produced. Reference-based alignment enabled detection of large structural variants and epigenetic modifications. De novo assembly of nanopore reads alone yielded a contiguous assembly (NG50 ~3 Mb). Next, we developed a protocol to generate ultra-long reads (N50 > 100kb, up to 882 kb). Incorporating an additional 5×-coverage of these data more than doubled the assembly contiguity (NG50 ~6.4 Mb). The final assembled genome was 2,867 million bases in size, covering 85.8% of the reference. Assembly accuracy, after incorporating complementary short-read sequencing data, exceeded 99.8%. Ultra-long reads enabled assembly and phasing of the 4 Mb major histocompatibility complex (MHC) locus in its entirety, measurement of telomere repeat length and closure of gaps in the reference human genome assembly GRCh38

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a triobased approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotyperesolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs

Illuminating G-Protein-Coupling Selectivity of GPCRs

Heterotrimetic G proteins consist of four subfamilies (Gs, Gi/o, Gq/11, and G12/13) that mediate signaling via G-protein-coupled receptors (GPCRs), principally by receptors binding Gα C termini. G-protein-coupling profiles govern GPCR-induced cellular responses, yet receptor sequence selectivity determinants remain elusive. Here, we systematically quantified ligand-induced interactions between 148 GPCRs and all 11 unique Gα subunit C termini. For each receptor, we probed chimeric Gα subunit activation via a transforming growth factor-α (TGF-α) shedding response in HEK293 cells lacking endogenous Gq/11 and G12/13 proteins, and complemented G-protein-coupling profiles through a NanoBiT-G-protein dissociation assay. Interrogation of the dataset identified sequence-based coupling specificity features, inside and outside the transmembrane domain, which we used to develop a coupling predictor that outperforms previous methods. We used the predictor to engineer designer GPCRs selectively coupled to G12. This dataset of fine-tuned signaling mechanisms for diverse GPCRs is a valuable resource for research in GPCR signaling

Illuminating G-Protein-Coupling Selectivity of GPCRs

Heterotrimetic G proteins consist of four subfamilies (Gs, Gi/o, Gq/11, and G12/13) that mediate signaling via G-protein-coupled receptors (GPCRs), principally by receptors binding G\u3b1 C termini. G-protein-coupling profiles govern GPCR-induced cellular responses, yet receptor sequence selectivity determinants remain elusive. Here, we systematically quantified ligand-induced interactions between 148 GPCRs and all 11 unique G\u3b1 subunit C termini. For each receptor, we probed chimeric G\u3b1 subunit activation via a transforming growth factor-\u3b1 (TGF-\u3b1) shedding response in HEK293 cells lacking endogenous Gq/11 and G12/13 proteins, and complemented G-protein-coupling profiles through a NanoBiT-G-protein dissociation assay. Interrogation of the dataset identified sequence-based coupling specificity features, inside and outside the transmembrane domain, which we used to develop a coupling predictor that outperforms previous methods. We used the predictor to engineer designer GPCRs selectively coupled to G12. This dataset of fine-tuned signaling mechanisms for diverse GPCRs is a valuable resource for research in GPCR signaling

Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Peart CR, Williams C, Pophaly SD, et al. Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Molecular Ecology Resources. 2021;21(7):2455-2470

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

De novo assembly of the cattle reference genome with single-molecule sequencing.

Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Platypus and echidna genomes reveal mammalian biology and evolution

Work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000), the National Key R&D Program of China (MOST) grant 2018YFC1406901, International Partnership Program of Chinese Academy of Sciences (152453KYSB20170002), Carlsberg foundation (CF16-0663) and Villum Foundation (25900) to G.Z. Q.Z. is supported by the National Natural Science Foundation of China (31722050, 31671319 and 32061130208), Natural Science Foundation of Zhejiang Province (LD19C190001), European Research Council Starting Grant (grant agreement 677696) and start-up funds from Zhejiang University. F.G., L.S.-W. and T.D. are supported by Australian Research Council (FT160100267, DP170104907 and DP110105396). M.B.R., J.C.F. and S.D.J. are supported by the Australian Research Council (LP160101728). We acknowledge the Kyoto University Research Administration Office for support and Human Genome Center, the Institute of Medical Science, the University of Tokyo for the super-computing resource for supporting T.H.’s research facilities. T.H. was financed by JSPS KAKENHI grant numbers 16K18630 and 19K16241 and the Sasakawa Scientific Research Grant from the Japan Science Society. The echidna RNA-sequencing analysis was supported by H.K.’s grant from the European Research Council (615253, OntoTransEvol). This work was supported by Guangdong Provincial Academician Workstation of BGI Synthetic Genomics No. 2017B090904014 (H.Y.), Robert and Rosabel Osborne Endowment, Howard Hughes Medical Institute (E.D.J.), Rockefeller University start-up funds (E.D.J.), Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R. and A.M.P.), Korea Health Technology R&D Project through the Korea Health Industry Development Institute HI17C2098 (A.R.). This work used the computational resources of BGI-Shenzhen and the NIH HPC Biowulf cluster (https://hpc.nih.gov). Animal icons are from https://www.flaticon.com/ (made by Freepik) and http://phylopic.org/