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生物燃料草种. 的基因组草图组装

Draft genome assembly of the biofuel grass crop .

机构信息

Earlham Institute, Norwich, NR4 7UZ, UK.

Institute of Biological, Environmental & Rural Sciences (IBERS) - Aberystwyth University, Aberystwyth, SY23 3EE, UK.

出版信息

F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. eCollection 2021.

Abstract

(Maxim.) Hack. is a highly productive C4 perennial rhizomatous biofuel grass crop. is among the most widely distributed species in the genus, particularly at cold northern latitudes, and is one of the progenitor species of the commercial genotypes. We generated a 2.54 Gb whole-genome assembly of the diploid cv. "Robustus 297" genotype, which represented ~59% of the expected total genome size. We later anchored this assembly using the chromosomes from the genome to generate a second assembly with improved contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored assemblies, respectively. We estimated our assemblies included ~85% of the genes based on homology and core markers. The utility of the new reference for genomic studies was evidenced by a 99% alignment rate of the RNA-seq reads from the same genotype.  The raw data, unanchored and anchored assemblies, and respective gene annotations are publicly available.

摘要

(马克西姆)杂种冰草是一种高产的 C4 多年生根茎型生物燃料草作物。它是该属中分布最广的物种之一,特别是在寒冷的北纬地区,也是商业杂种冰草基因型的祖先生物种之一。我们生成了二倍体 cv. “Robustus 297”基因型的 25.4 千兆碱基的全基因组组装,这代表了预期总基因组大小的~59%。我们后来使用来自 cv. “Maximowiczii”基因组的染色体来锚定这个组装,以生成具有改进连续性的第二个组装。我们分别在未锚定和锚定的组装中注释了 86767 个和 69049 个蛋白质编码基因。我们基于同源性和核心标记估计我们的组装包含了大约 85%的 cv. “Maximowiczii”基因。新参考基因组对基因组研究的实用性通过同一基因型的 RNA-seq reads 的 99%比对率得到证明。原始数据、未锚定和锚定组装以及各自的基因注释均公开可用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4333/7921889/2ca5fc2a6780/f1000research-10-47786-g0000.jpg

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