Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.

IF 2.8 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Peter Z Schall, Jeffrey M Kidd
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引用次数: 0

Abstract

Structural variation makes an important contribution to canine evolution and phenotypic differences. Although recent advances in long-read sequencing have enabled the generation of multiple canine genome assemblies, most prior analyses of structural variation have relied on short-read sequencing. To offer a more complete assessment of structural variation in canines, we performed an integrative analysis of structural variants present in 12 canine samples with available long-read and short-read sequencing data along with genome assemblies. Use of long-reads permits the discovery of heterozygous variation that is absent in existing haploid assembly representations while offering a marked increase in the ability to identify insertion variants relative to short-read approaches. Examination of the size spectrum of structural variants shows that dimorphic LINE-1 and SINE variants account for over 45% of all deletions and identified 1,410 LINE-1s with intact open reading frames that show presence-absence dimorphism. Using a graph-based approach, we genotype newly discovered structural variants in an existing collection of 1,879 resequenced dogs and wolves, generating a variant catalog containing a 56.5% increase in the number of deletions and 705% increase in the number of insertions previously found in the analyzed samples. Examination of allele frequencies across admixture components present across breed clades identified 283 structural variants evolving with a signature of selection.

利用长读和短读数据进行犬结构变异的综合基因分型和分析。
结构变异在犬类进化和表型差异中起着重要作用。尽管最近在长读测序方面的进展已经能够产生多个犬基因组组装,但大多数先前的结构变异分析都依赖于短读测序。为了对犬科动物的结构变异进行更全面的评估,我们对12个犬科动物样本的结构变异进行了综合分析,包括长读和短读测序数据以及基因组组装。使用长读取允许发现杂合变异,这在现有的单倍体组装表示中是不存在的,同时提供了相对于短读取方法识别插入变异的能力的显着增加。对结构变异的大小谱的检查表明,二态的LINE-1和SINE变异占所有缺失的45%以上,并鉴定出1,410个具有完整开放阅读框的LINE-1,显示存在-缺失二态性。使用基于图的方法,我们在现有的1879只狗和狼的重测序集合中对新发现的结构变异进行了基因分型,生成了一个变异目录,其中缺失数量增加了56.5%,插入数量增加了705%。对跨品种分支的混合成分的等位基因频率进行检查,发现283个结构变异具有选择的特征。
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来源期刊
Genome Biology and Evolution
Genome Biology and Evolution EVOLUTIONARY BIOLOGY-GENETICS & HEREDITY
CiteScore
5.80
自引率
6.10%
发文量
169
审稿时长
1 months
期刊介绍: About the journal Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics. Papers considered for publication report novel evolutionary findings that concern natural genome diversity, population genomics, the structure, function, organisation and expression of genomes, comparative genomics, proteomics, and environmental genomic interactions. Major evolutionary insights from the fields of computational biology, structural biology, developmental biology, and cell biology are also considered, as are theoretical advances in the field of genome evolution. GBE’s scope embraces genome-wide evolutionary investigations at all taxonomic levels and for all forms of life — within populations or across domains. Its aims are to further the understanding of genomes in their evolutionary context and further the understanding of evolution from a genome-wide perspective.
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