A chromosome-scale assembly for ‘d’Anjou’ pear
A chromosome-scale assembly for ‘d’Anjou’ pear
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DOI：
10.1093/g3journal/jkae003
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发表时间：
2023-08
期刊：
影响因子：
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通讯作者：
Alan E. Yocca;M. Akinyuwa;Nick P. Bailey;Brannan R Cliver;Harrison Estes;Abigail Guillemette;
中科院分区：
文献类型：
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作者：
Alan E. Yocca;M. Akinyuwa;Nick P. Bailey;Brannan R Cliver;Harrison Estes;Abigail Guillemette;
栽培梨由几个梨属物种组成，其中P. communis（欧洲梨）占全球产量的很大一部分。作为一种相对较新的驯化作物和多年生树木，梨可以从基因组辅助育种中受益。此外，蔷薇科内的比较基因组学有望更好地了解这个经济上重要的家庭内的进化。在这里，我们产生了一个全相位的染色体规模的基因组组装的P. communis cv。"安茹“。使用PacBio HiFi和Dovetail Omni-C读数，基因组被解析为预期的17条染色体，每个单倍型总计近540兆碱基，重叠群N50近14 Mb。这两种单倍型彼此高度同线性，并且与苹果‘蜜脆’苹果基因组高度同线性。在每个单倍型中注释了近45，000个基因，其中超过90%具有直接的RNA-seq表达证据。我们检测到苹果和梨之间共享的已知全基因组重复的签名，我们估计57%的d 'Anjou基因保留在来自该事件的重复中。该基因组突出了产生定相二倍体组装体用于在高度杂合作物物种中恢复完全等位基因互补的价值。
Cultivated pear consists of several Pyrus species with P. communis (European pear) representing a large fraction of worldwide production. As a relatively recently domesticated crop and perennial tree, pear can benefit from genome-assisted breeding. Additionally, comparative genomics within Rosaceae promises greater understanding of evolution within this economically important family. Here, we generate a fully-phased chromosome-scale genome assembly of P. communis cv. ‘d’Anjou’. Using PacBio HiFi and Dovetail Omni-C reads, the genome is resolved into the expected 17 chromosomes, with each haplotype totalling nearly 540 Megabases and a contig N50 of nearly 14 Mb. Both haplotypes are highly syntenic to each other, and to the Malus domestica ‘Honeycrisp’ apple genome. Nearly 45,000 genes were annotated in each haplotype, over 90% of which have direct RNA-seq expression evidence. We detect signatures of the known whole-genome duplication shared between apple and pear, and we estimate 57% of d’Anjou genes are retained in duplicate derived from this event. This genome highlights the value of generating phased diploid assemblies for recovering the full allelic complement in highly heterozygous crop species.