TRTech-PGR: Improvement of the genome sequence assembly of Chinese Spring wheat

普通面包小麦是全球两种最重要的作物之一，在该国的经济重要性排名第三。小麦基因组参考序列是小麦遗传育种的重要资源。期待已久的面包小麦品种中国春（CS）的基因组序列最近由一个国际科学家联盟公布。自20世纪50年代以来，CS栽培品种一直作为遗传模型，其基因组序列有望作为小麦基因组的参考。考虑到小麦基因组的大小是人类基因组的五倍，全序列是一项了不起的成就。为了充分利用基因组的价值，该项目继续利用最新的技术进步来改进已公布的基因组，这些技术进步将通过填补空白和解决组装中的不一致性来进一步改进序列。该序列将用于分析小麦基因组的结构和进化，并将提供给其他人，以识别和编目序列中的所有基因。国际小麦基因组测序联盟（IWGSC）最近公布了中国春小麦（CS）基因组序列（IWGSC RefSeq v1.0），作为小麦基因组的参考。该序列是一个全基因组霰弹枪、短读组装，剩余的空白可以通过使用长读测序技术和Bionano光学图谱来填补。为了改进序列，将IWGSC RefSeq v1.0假分子分解成支架，并使用光学图谱检测和解析嵌合支架，以锚未分配的支架，并校正支架和超级支架的位置和方向的模糊性。CS基因组的长读段组装（Falcon Triticum 1.0）将用于闭合缺口。遗传图谱和光学图谱将用于重建21条小麦染色体的假分子。假分子将用于小麦基因组结构和进化的分析。该序列将通过项目网站公开，并将发布到NCBI和IWGSC数据库。与IWGSC合作，基因将在新序列中重新注释。将在GrainGenes上以及通过出版物和科学会议上的演讲传播对该序列的认识。该项目将为从事生物信息学工作的博士后学者和年轻科学家提供极好的培训机会。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Common bread wheat is globally one of the two most important crops and is third in economic importance in this country. A reference-quality genome sequence for wheat is an essential resource for advancing wheat genetics and breeding. The long-awaited sequence of the genome of bread wheat cultivar Chinese Spring (CS) was recently published by an international consortium of scientists. The CS cultivar has served as a genetic model since the 1950s, and the sequence of its genome is expected to serve as a reference for the wheat genome. Considering the large size of the wheat genome, which is five times the size of the human genome, the full sequence was a remarkable accomplishment. To fully leverage the value of the genome, this project continues improving the published genome by making use of recent technological advances that will further improve the sequence by filling gaps and resolving inconsistencies in the assembly. The sequence will be used to analyze the structure and evolution of the wheat genome and will be provided to others to identify and catalogue all of the genes in the sequence. The sequence will be made publicly available and will serve an excellent training ground for young scientists in genomics.The International Wheat Genome Sequencing Consortium (IWGSC) recently published the assembly of the bread wheat cv Chinese Spring (CS) genome sequence (IWGSC RefSeq v1.0), to serve as a reference for the wheat genome. The sequence was a whole-genome-shotgun, short-read assembly with remaining gaps that could be filled by making use of long-read sequencing technology and of Bionano optical maps. To improve the sequence, the IWGSC RefSeq v1.0 pseudomolecules will be disassembled into scaffolds, and optical maps will be used to detect and resolve chimeric scaffolds, to anchor unassigned scaffolds, and to correct ambiguities in positions and orientations of scaffolds and super-scaffolds. A long-read assembly of the CS genome (Falcon Triticum 1.0) will be used to close gaps. Genetic and optical maps will be used to reconstruct the pseudomolecules of the 21 wheat chromosomes. The pseudomolecules will be employed in the analyses of structure and evolution of the wheat genome. The sequence will be made publicly available through a project website, and will be released to the NCBI and IWGSC databases. In collaboration with the IWGSC, genes will be reannotated in the new sequence. Awareness about the sequence will be disseminated on GrainGenes and via publications and presentations in scientific meetings. The project will afford excellent training opportunities for postdoctoral scholars and young scientists carrying out the bioinformatics work.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.