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  • Cold Spring Harbor Laboratory  (4)
  • Medicine  (4)
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  • Cold Spring Harbor Laboratory  (4)
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  • Medicine  (4)
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  • 1
    Online Resource
    Online Resource
    Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
    Cold Spring Harbor Laboratory ; 2022
    In:  Genome Research Vol. 32, No. 9 ( 2022-09), p. 1669-1684
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 32, No. 9 ( 2022-09), p. 1669-1684
    Abstract: Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali ( O . ammon polii , 2 n = 56), a female Tibetan sheep ( O . aries , 2 n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2 n = 54 than with 2 n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C 〉 A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F 2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.276769.122
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2022
    detail.hit.zdb_id: 1483456-X
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 2
    Online Resource
    Online Resource
    Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature
    Cold Spring Harbor Laboratory ; 2021
    In:  Genome Research Vol. 31, No. 4 ( 2021-04), p. 622-634
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 31, No. 4 ( 2021-04), p. 622-634
    Abstract: Heterosis or hybrid vigor is a common phenomenon in plants and animals; however, the molecular mechanisms underlying heterosis remain elusive, despite extensive studies on the phenomenon for more than a century. Here we constructed a large collection of F1 hybrids of Saccharomyces cerevisiae by spore-to-spore mating between homozygous wild strains of the species with different genetic distances and compared growth performance of the F1 hybrids with their parents. We found that heterosis was prevalent in the F1 hybrids at 40°C. A hump-shaped relationship between heterosis and parental genetic distance was observed. We then analyzed transcriptomes of selected heterotic and depressed F1 hybrids and their parents growing at 40°C and found that genes associated with one-carbon metabolism and related pathways were generally up-regulated in the heterotic F1 hybrids, leading to improved cellular redox homeostasis at high temperature. Consistently, genes related with DNA repair, stress responses, and ion homeostasis were generally down-regulated in the heterotic F1 hybrids. Furthermore, genes associated with protein quality control systems were also generally down-regulated in the heterotic F1 hybrids, suggesting a lower level of protein turnover and thus higher energy use efficiency in these strains. In contrast, the depressed F1 hybrids, which were limited in number and mostly shared a common aneuploid parental strain, showed a largely opposite gene expression pattern to the heterotic F1 hybrids. We provide new insights into molecular mechanisms underlying heterosis and thermotolerance of yeast and new clues for a better understanding of the molecular basis of heterosis in plants and animals.
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.262055.120
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2021
    detail.hit.zdb_id: 1483456-X
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 3
    Online Resource
    Online Resource
    Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
    Cold Spring Harbor Laboratory ; 2010
    In:  Genome Research Vol. 20, No. 9 ( 2010-09), p. 1238-1249
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 20, No. 9 ( 2010-09), p. 1238-1249
    Abstract: The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA-seq). In this study, we applied RNA-seq to globally sample transcripts of the cultivated rice Oryza sativa indica and japonica subspecies for resolving the whole-genome transcription profiles. We identified 15,708 novel transcriptional active regions (nTARs), of which 51.7% have no homolog to public protein data and 〉 63% are putative single-exon transcripts, which are highly different from protein-coding genes ( 〈 20%). We found that ∼48% of rice genes show alternative splicing patterns, a percentage considerably higher than previous estimations. On the basis of the available rice gene models, 83.1% (46,472 genes) of the current rice gene models were validated by RNA-seq, and 6228 genes were identified to be extended at the 5′ and/or 3′ ends by at least 50 bp. Comparative transcriptome analysis demonstrated that 3464 genes exhibited differential expression patterns. The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution.
    Type of Medium: Online Resource
    ISSN: 1088-9051
    URL: Article
    DOI: 10.1101/gr.106120.110
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2010
    detail.hit.zdb_id: 1483456-X
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
  • 4
    Online Resource
    Online Resource
    Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
    Cold Spring Harbor Laboratory ; 2020
    In:  Genome Research Vol. 30, No. 1 ( 2020-01), p. 118-126
    Details
    In: Genome Research, Cold Spring Harbor Laboratory, Vol. 30, No. 1 ( 2020-01), p. 118-126
    Abstract: Genome editing by the well-established CRISPR/Cas9 technology has greatly facilitated our understanding of many biological processes. However, a complete whole-genome knockout for any species or model organism has rarely been achieved. Here, we performed a systematic knockout of all the genes (1333) on Chromosome 1 in zebrafish, successfully mutated 1029 genes, and generated 1039 germline-transmissible alleles corresponding to 636 genes. Meanwhile, by high-throughput bioinformatics analysis, we found that sequence features play pivotal roles in effective gRNA targeting at specific genes of interest, while the success rate of gene targeting positively correlates with GC content of the target sites. Moreover, we found that nearly one-fourth of all mutants are related to human diseases, and several representative CRISPR/Cas9-generated mutants are described here. Furthermore, we tried to identify the underlying mechanisms leading to distinct phenotypes between genetic mutants and antisense morpholino-mediated knockdown embryos. Altogether, this work has generated the first chromosome-wide collection of zebrafish genetic mutants by the CRISPR/Cas9 technology, which will serve as a valuable resource for the community, and our bioinformatics analysis also provides some useful guidance to design gene-specific gRNAs for successful gene editing.
    Type of Medium: Online Resource
    ISSN: 1088-9051 , 1549-5469
    URL: Article
    DOI: 10.1101/gr.248559.119
    RVK:
    XA 10000
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2020
    detail.hit.zdb_id: 1483456-X
    SSG: 12
    Location Call Number Limitation Availability
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    Online Resource
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