Genome sequence of the olive tree, Olea europaea.
Genome sequence of the olive tree, Olea europaea.
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DOI：
10.1186/s13742-016-0134-5
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发表时间：
2016-06-27
期刊：
影响因子：
9.2
通讯作者：
Gabaldón T
中科院分区：
文献类型：
--
作者：
Cruz F;Julca I;Gómez-Garrido J;Loska D;Marcet-Houben M;Cano E;Galán B;Frias L;Ribeca P;Derdak S;Gut M;Sánchez-Fernández M;García JL;Gut IG;Vargas P;Alioto TS;Gabaldón T
地中海橄榄（Olea europaea subsp.）欧洲橄榄树（Europaea）是最早被驯化的树木之一，目前在地中海地区作为橄榄油的来源具有重要的农业意义。驯化品种之间的表型差异，或驯化橄榄树和它们的野生亲属之间的分子基础，仍然知之甚少。野生和栽培橄榄树都有46条染色体（2n）。来自全基因组鸟枪测序的总共543 Gb的原始DNA序列，以及包含来自1,000多年的橄榄树（cv. Farga）通过Illumina测序使用配对和配对末端文库的不同组合产生。组装得到具有443 kb的支架N50和1.31Gb的总长度的最终基因组，其代表估计的基因组长度（1.38Gb）的95%。此外，相关真菌出芽短梗霉部分测序。基因组注释，在不同阶段的叶，根和果实组织的RNA测序的辅助下，产生了56，349个独特的蛋白质编码基因，表明最近的基因组扩增。使用CEGMA管道估计的基因组完整性达到98.79%。构建了O.欧洲树将为研究这一重要树种的进化和驯化过程提供宝贵的资源，并可确定关键表型性状的遗传基础。此外，它将加强育种计划和新品种的形成。
The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidiumpullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.