Chromosome-level reference genome for European flat oyster (Ostrea edulis L.).
Chromosome-level reference genome for European flat oyster (Ostrea edulis L.).
复制标题
DOI：
10.1111/eva.13460
复制
发表时间：
2022-11
影响因子：
4.1
通讯作者：
中科院分区：
文献类型：
--
作者：
欧洲平牡蛎 (Ostrea edulis L.) 是一种自然分布在欧洲各地的双壳类动物，几个世纪以来一直是人类饮食中不可或缺的一部分，直到人类活动和疾病爆发导致野生种群严重减少。尽管人们对支持种群管理和水产养殖的遗传应用越来越感兴趣，但迄今为止仍缺乏该物种的参考基因组。在这里，我们报告了使用 Oxford Nanopore、Illumina、Dovetail OmniC™ 邻近连接和 RNA 测序生成的欧洲扁平牡蛎基因组的染色体水平组装和注释。将重叠群组装体（N50：2.38Mb）搭建成10条假染色体的预期核型。最终组装的大小为 935.13Mb，支架 N50 为 95.56Mb，预测的重复景观主要由 O. edulis 特有的未分类元素主导。使用多种方法验证了组装的准确性和完整性，包括使用 ddRAD-Seq 技术构建的新颖连锁图，其中包含来自四个全同胞家族（8 个父母和 163 个 F1 后代）的 4016 个 SNP。整合多组织转录组数据、比较蛋白质证据和从头算基因预测的基因组注释确定了 35,699 个蛋白质编码基因。多个高质量双壳类基因组组装证明了染色体水平的同线性，其中包括为法国美味O. edulis个体独立生成的O. edulis基因组。比较基因组学被用来描述牡蛎进化过程中基因家族扩张的特征，这可能促进适应。这个欧洲扁平牡蛎的新参考基因组将使高分辨率基因组学成为可能，以支持保护和水产养殖计划，并提高我们对双壳类基因组进化的理解。
The European flat oyster (Ostrea edulis L.) is a bivalve naturally distributed across Europe, which was an integral part of human diets for centuries, until anthropogenic activities and disease outbreaks severely reduced wild populations. Despite a growing interest in genetic applications to support population management and aquaculture, a reference genome for this species is lacking to date. Here, we report a chromosome‐level assembly and annotation for the European Flat oyster genome, generated using Oxford Nanopore, Illumina, Dovetail OmniC™ proximity ligation and RNA sequencing. A contig assembly (N50: 2.38 Mb) was scaffolded into the expected karyotype of 10 pseudochromosomes. The final assembly is 935.13 Mb, with a scaffold‐N50 of 95.56 Mb, with a predicted repeat landscape dominated by unclassified elements specific to O. edulis. The assembly was verified for accuracy and completeness using multiple approaches, including a novel linkage map built with ddRAD‐Seq technology, comprising 4016 SNPs from four full‐sib families (eight parents and 163 F1 offspring). Annotation of the genome integrating multitissue transcriptome data, comparative protein evidence and ab‐initio gene prediction identified 35,699 protein‐coding genes. Chromosome‐level synteny was demonstrated against multiple high‐quality bivalve genome assemblies, including an O. edulis genome generated independently for a French O. edulis individual. Comparative genomics was used to characterize gene family expansions during Ostrea evolution that potentially facilitated adaptation. This new reference genome for European flat oyster will enable high‐resolution genomics in support of conservation and aquaculture initiatives, and improves our understanding of bivalve genome evolution.
登录
查看更多内容
DOI：
10.1093/database/bas019
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Attwood TK;Coletta A;Muirhead G;Pavlopoulou A;Philippou PB;Popov I;Romá-Mateo C;Theodosiou A;Mitchell AL
通讯作者：
Mitchell AL
通过高精度和完整的纠错，高效组装纳米孔读数。
影响因子：
16.6
作者：
Chen Y;Nie F;Xie SQ;Zheng YF;Dai Q;Bray T;Wang YX;Xing JF;Huang ZJ;Wang DP;He LJ;Luo F;Wang JX;Liu YZ;Xiao CL
通讯作者：
Xiao CL
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
10.7
作者：
Minh BQ;Nguyen MA;von Haeseler A
通讯作者：
von Haeseler A
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ