Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of  Brassica napus

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Abstract

Rapeseed ( Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

Abstract

The assembly of eight high-quality rapeseed genomes allows identification of presence and absence variations (PAVs) and small variations. PAV-based genome-wide association analysis uncovered causal variations for agronomic traits and ecotype differentiation.

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Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

H Tettelin, V Masignani, M. J. Cieslewicz … (2005)

The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.

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Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.

Christopher Carlson, Michael A Eberle, Mark J. Rieder … (2004)

Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing common polymorphism is inefficient, because genotypes at many of these sites are strongly correlated. Thus, it is not necessary to assay all common variants if the patterns of allelic association between common variants can be described. We have developed an algorithm to select the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies, such that all known common polymorphisms either are directly assayed or exceed a threshold level of association with a tagSNP. The algorithm is based on the r(2) linkage disequilibrium (LD) statistic, because r(2) is directly related to statistical power to detect disease associations with unassayed sites. We show that, at a relatively stringent r(2) threshold (r2>0.8), the LD-selected tagSNPs resolve >80% of all haplotypes across a set of 100 candidate genes, regardless of recombination, and tag specific haplotypes and clades of related haplotypes in nonrecombinant regions. Thus, if the patterns of common variation are described for a candidate gene, analysis of the tagSNP set can comprehensively interrogate for main effects from common functional variation. We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries.

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Is Open Access

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Xiangchao Gan, Oliver Stegle, Jonas Behr … (2011)

Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions.

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Author and article information

Contributors

Kede Liu:

ORCID: http://orcid.org/0000-0002-1395-2049

kdliu@mail.hzau.edu.cn

Qing-Yong Yang:

ORCID: http://orcid.org/0000-0002-3510-8906

yqy@mail.hzau.edu.cn

Ling-Ling Chen:

ORCID: http://orcid.org/0000-0002-3005-526X

llchen@mail.hzau.edu.cn

Liang Guo:

ORCID: http://orcid.org/0000-0001-7191-5062

guoliang@mail.hzau.edu.cn

Journal

Journal ID (nlm-ta): Nat Plants

Journal ID (iso-abbrev): Nat Plants

Title: Nature Plants

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2055-0278

Publication date (Electronic): 13 January 2020

Publication date PMC-release: 13 January 2020

Publication date (Print): 2020

Volume: 6

Issue: 1

Pages: 34-45

Affiliations

[1 ]ISNI 0000 0004 1790 4137, GRID grid.35155.37, National Key Laboratory of Crop Genetic Improvement, , Huazhong Agricultural University, ; Wuhan, People’s Republic of China

[2 ]ISNI 0000 0004 1790 4137, GRID grid.35155.37, Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, , Huazhong Agricultural University, ; Wuhan, People’s Republic of China

Author information

Chaocheng Guo http://orcid.org/0000-0001-7955-4222

Kede Liu http://orcid.org/0000-0002-1395-2049

Qing-Yong Yang http://orcid.org/0000-0002-3510-8906

Ling-Ling Chen http://orcid.org/0000-0002-3005-526X

Liang Guo http://orcid.org/0000-0001-7191-5062

Article

Publisher ID: 577

DOI: 10.1038/s41477-019-0577-7

PMC ID: 6965005

PubMed ID: 31932676

SO-VID: 41c828bc-e8ca-4bf9-8864-c1c87ec8e0c6

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 31 July 2019

Date accepted : 29 November 2019

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Keywords: genetics,plant sciences,agriculture

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Keywords: genetics, plant sciences, agriculture

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Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

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Most cited references 40

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium.

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

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