CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome.
CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome.
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CGT-seq：表观基因组引导的核心基因组从头组装，适用于具有大基因组的不同群体
DOI：
10.1093/nar/gky522
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发表时间：
2018-10-12
影响因子：
14.9
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Qi M;Li Z;Liu C;Hu W;Ye L;Xie Y;Zhuang Y;Zhao F;Teng W;Zheng Q;Fan Z;Xu L;Lang Z;Tong Y;Zhang Y
摘要植物的遗传多样性非常高。最近对67份水稻材料进行了全基因组测序，发现了10，872个新基因。不同群体之间或作物与野生近缘种之间的遗传结构比较对于获得决定关键性状的功能组分是必不可少的。然而，许多主要作物具有千兆碱基规模的基因组，这并不适合WGS。现有的具有成本效益的测序方法包括重测序、外显子组测序和基于限制性内切酶的方法都难以从具有大基因组大小的高度分化的群体中获得长的新基因组序列。本研究提出了一种不依赖参考的核心基因组靶向测序方法CGT-seq，该方法利用来自活性和抑制性表观遗传标记的表观基因组信息来指导主要由启动子和基因内区域组成的核心基因组的组装。该方法相对容易实现，并且对于捕获面包小麦的核心基因组显示出高灵敏度和特异性。CGT-seq read覆盖了小麦95%的基因内区域和89%的启动子区域。我们在水稻中进一步证明，CGT-seq从以前未测序的生态型中捕获了数百个新基因和调控序列。结合基因内和附近区域的特异性富集和测序，CGT-seq是一种节省时间和资源的方法，可用于分析具有大基因组的测序和非测序群体中的功能相关区域。
Abstract Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.
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影响因子：
46.9
作者：
通讯作者：
--
影响因子：
64.8
作者：
Luo MC;Gu YQ;Puiu D;Wang H;Twardziok SO;Deal KR;Huo N;Zhu T;Wang L;Wang Y;McGuire PE;Liu S;Long H;Ramasamy RK;Rodriguez JC;Van SL;Yuan L;Wang Z;Xia Z;Xiao L;Anderson OD;Ouyang S;Liang Y;Zimin AV;Pertea G;Qi P;Bennetzen JL;Dai X;Dawson MW;Müller HG;Kugler K;Rivarola-Duarte L;Spannagl M;Mayer KFX;Lu FH;Bevan MW;Leroy P;Li P;You FM;Sun Q;Liu Z;Lyons E;Wicker T;Salzberg SL;Devos KM;Dvořák J
通讯作者：
Dvořák J
影响因子：
7
作者：
Jackman, Shaun D.;Vandervalk, Benjamin P.;Birol, Inanc
通讯作者：
Birol, Inanc
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
30.8
作者：
Chia, Jer-Ming;Song, Chi;Ware, Doreen
通讯作者：
Ware, Doreen