A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.
A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.
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DOI：
10.1093/gigascience/giy094
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发表时间：
2018-08-01
期刊：
影响因子：
9.2
通讯作者：
Bassil NV
中科院分区：
文献类型：
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作者：
VanBuren R;Wai CM;Colle M;Wang J;Sullivan S;Bushakra JM;Liachko I;Vining KJ;Dossett M;Finn CE;Jibran R;Chagné D;Childs K;Edger PP;Mockler TC;Bassil NV
大多数植物基因组草图的碎片化性质阻碍了下游基因发现、育种性状定位和其他功能基因组学应用。迫切需要改进或完成植物基因组组装草图。在这里，我们提出了一个染色体规模的装配黑树莓基因组使用单分子实时太平洋生物科学测序和高通量染色质构象捕获（Hi-C）基因组支架。更新后的V3组装体具有5.1 Mb的重叠群N50，比之前基于Illumina的版本提高了200倍。235个重叠群中的每一个都被锚定并定向到七条染色体中，纠正了几个主要的错误组装。黑树莓V3含有47 Mb的新序列，包括大的近着丝粒区域和数千个以前未注释的蛋白质编码基因。在这些新基因中，有数百个扩展的串联基因阵列，它们在基于Illumina的组装中被折叠。详细的比较基因组学与高品质的V4林地草莓基因组（草莓）揭示了近乎完美的1：1同线性与串联基因阵列组成的显着分歧。黑树莓谱系特异性串联基因阵列与抗病性、次生代谢物生物合成等农艺性状相关。串联基因阵列分辨率的提高突出了在植物基因组草案中重新组装这些高度复杂且具有生物学重要性的区域的需要。更新后的高质量黑树莓参考基因组将用于园艺上重要的蔷薇科家族的比较基因组学，并使标记辅助育种的发展成为可能。
The fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies. Here, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis. The improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.