Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

Tian, Xiaomeng; Li, Ran; Fu, Weiwei; Li, Yan; Wang, Xihong; Li, Ming; Du, Duo; Tang, Qianzi; Cai, Yi; Long, Yiming; Zhao, Yue; Li, Mingzhou; Jiang, Yu

doi:10.1007/s11427-019-9551-7

Cited by 59 publications

(63 citation statements)

References 61 publications

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“…In Eukaryotes, pan-genomes have been occasionally reported in plants, fungi, and microalgae, where they have been often associated with the development of phenotypic traits linked with environmental adaptation, resistance to diseases, and intraspecific differentiation [30][31][32][33][34][35][36]. Although a few studies have recently extended the pangenome concept to the animal kingdom, to the best of our knowledge, these have so far mostly linked the dispensable fraction of animal genomes with intergenic regions, bringing little evidence in support of the association between accessory genomic regions and gene PAV with adaptation [37][38][39].…”

Section: Introductionmentioning

confidence: 99%

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

et al. 2020

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Background The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Results Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Conclusions Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.

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Section: Introductionmentioning

confidence: 99%

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

et al. 2020

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“…However, their genome differences were not well understood. Especially, the studies of the large genomic structural variations just emerged recently [ 10 – 12 ]. Copy number variation (CNV) is a kind of large genomic structural variations, which ranges from 50 base pairs (bp) to 5 million base pairs (Mbp) [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative analyses of copy number variations between Bos taurus and Bos indicus

Xia

et al. 2020

BMC Genomics

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Background Bos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. Results Based on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage. Conclusions This study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

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“…In addition, the pangenome offers a natural replacement for the current paradigm of using a single reference genome, as the choice of the reference affects downstream genomic analyses, including GWAS and gene expression quantification (Gage et al, 2019). Using pangenome as a reference improves read mapping and variant calling accuracy (Eggertsson et al, 2017;Garrison et al, 2018;Kim et al, 2019;Tian et al, 2019). The adoption of the pangenome reference will also allow the inclusion of variants beyond SNPs in GWAS.…”

Section: Beyond Single Reference Genomics -The Pan-genome Approachmentioning

confidence: 99%

Global Role of Crop Genomics in the Face of Climate Change

et al. 2020

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The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

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Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data

Cited by 59 publications

References 61 publications

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

Comparative analyses of copy number variations between Bos taurus and Bos indicus

Global Role of Crop Genomics in the Face of Climate Change

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