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

普通面包用小麦是全球最重要的两种作物之一，在该国的经济重要性排名第三。小麦基因组序列是推进小麦遗传育种的重要资源。一个国际科学家联盟最近公布了人们期待已久的面包小麦品种中国春（CS）的基因组序列。自20世纪50年代以来，CS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5倍，完整的序列是一个了不起的成就。为了充分利用基因组的价值，该项目将继续利用最新的技术进步来改进已发表的基因组，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，并将提供给其他人识别和编目序列中的所有基因。该序列将向公众开放，并将为基因组学领域的年轻科学家提供一个极好的培训基地。国际小麦基因组测序联盟（IWGSC）最近公布了面包小麦中国春（CS）基因组序列的组装（IWGSC RefSeq v1.0），以作为小麦基因组的参考。该序列是全基因组霰弹枪式的短读序列，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伪分子拆解成支架，并利用光学图谱检测和解析嵌合支架，锚定未分配支架，纠正支架和超级支架位置和方向的模糊性。CS基因组的长读汇编（Falcon Triticum 1.0）将用于填补空白。遗传和光学图谱将用于重建21条小麦染色体的假分子。这些伪分子将用于分析小麦基因组的结构和进化。该序列将通过项目网站公开，并将发布到NCBI和IWGSC数据库中。与IWGSC合作，基因将在新序列中重新注释。有关序列的认识将在GrainGenes上传播，并通过出版物和科学会议上的演讲来传播。本项目将为从事生物信息学工作的博士后学者和青年科学家提供良好的培训机会。该奖项反映了美国国家科学基金会的法定使命，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.