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The Tartary Buckwheat genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance

Molecular Plant 2017年第9期10卷 1224-1237页

作者： Zhang, Lijun Li, Xiuxiu Ma, Bin Gao, Qiang Du, Huilong Han, Yuanhuai Li, Yan Cao, Yinghao Qi, Ming Zhu, Yaxin Lu, Hongwei Ma, Mingchuan Liu, Longlong Zhou, Jianping Nan, Chenghu Qin, Yongjun Wang, Jun Cui, Lin Liu, Huimin Liang, Chengzhi Qiao, Zhijun Shanxi Acad Agr Sci Inst Crop Germplasm Resources Res Taiyuan 030031 Shanxi Peoples R China Minist Agr Key Lab Crop Gene Resources & Germplasm Enhanceme Taiyuan 030031 Shanxi Peoples R China Shanxi Key Lab Genet Resources & Genet Improvemen Taiyuan 030031 Shanxi Peoples R China Chinese Acad Sci Inst Genet & Dev Biol State Key Lab Plant Genom Beijing 100101 Peoples R China Univ Chinese Acad Sci Coll Life Sci Beijing 100049 Peoples R China Shanxi Agr Univ Coll Agron Taiyuan 030801 Shanxi Peoples R China Chinese Acad Sci Inst Microbiol State Key Lab Microbial Resources Beijing Peoples R China South China Agr Univ Coll Marine Sci Guangzhou 510642 Guangdong Peoples R China

Tartary buckwheat （Fagopyrum tataricum） is an important pseudocereal crop that is strongly adapted to growth in adverse environments. Its gluten-free grain contains complete proteins with a well-balanced composition of essential amino acids and is a rich source of beneficial phytochemicals that provide significant health benefits. Here, we report a high-quality, chromosome-scale Tartary buckwheat genome sequence of- 489.3 Mb that is assembled by combining whole-genome shotgun sequencing of both Illumina short reads and single-molecule real-time long reads, sequence tags of a large DNA insert fosmid library, Hi-C sequencing data, and BioNano genome maps. We annotated 33 366 high-confidence protein-coding genes based on expression evidence. Comparisons of the intra-genome with the sugar beet genome revealed an independent whole-genome duplication that occurred in the buckwheat lineage after they diverged from the common ancestor, which was not shared with rosids or asterids. The reference genome facilitated the identification of many new genes predicted to be involved in rutin biosynthesis and regulation, aluminum stress resistance, and in drought and cold stress responses. Our data suggest that Tartary buckwheat＇s ability to tolerate high levels of abiotic stress is attributed to the expansion of several gene families involved in signal transduction, gene regulation, and membrane transport. The availability of these genomic resources will facilitate the discovery of agronomically and nutritionally important genes and genetic improvement of Tartary buckwheat.

关键词： tartary buckwheat de novo genome assembly rutin biosynthesis aluminum resistance abiotic stress,whole genome duplication

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Draft genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 501-514页

作者： Jingqi Zhou Ake Liu Funan He Yunbin Zhang Libing Shen Jun Yu Xiang Zhang School of Public Health Shanghai Jiao Tong University School of MedicineShanghai 200025China department of Life Sciences Changzhi UniversityChangzhi 046011China Greehey Children’s Cancer Research Institute UT Health San AntonioSan AntonioTX 78229USA State Key Laboratory of Cell Biology Shanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai 200031China International Human Phenome Institutes(Shanghai) Shanghai 200433China Institute of Neuroscience Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Shanghai Nanmulin Biotechnology Company Limited Shanghai 200031China

The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River *** a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available,*** provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton *** this study,we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds,with contig N50 of 3937 kb and scaffold N50 of 5675 kb in *** analysis shows that *** is a slow-evolving fish that diverged from elephant sharks about 96 million years ***,two gene families related to the immune system(immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in *** *** also identified the Hox gene clusters in *** and discovered that seven Hox genes shared by five representative fish species are missing in *** RNA sequencing data from *** and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to *** functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both *** and Callorhinchus milii)could partly explain the absence of hard bone in their ***,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of ***,as well as the genome evolution in cartilaginous fishes.

关键词： White-blotched river stingray Potamotrygon leopoldi de novo genome assembly Vitamin D-binding protein Niche adaptation

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High-quality genome assembly of Huazhan and Tianfeng,the parents of an elite rice hybrid Tian-you-hua-zhan

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Science China(Life Sciences) 2022年第2期65卷 398-411页

作者： Hui Zhang Yuexing Wang Ce deng Sheng Zhao Peng Zhang Jie Feng Wei Huang Shujing Kang Qian Qian Guosheng Xiong Yuxiao Chang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life SciencesSouth China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China National Key Laboratory of Wheat and Maize Crop Science College of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Life Science and Technology Guangxi UniversityNanning 530004China Plant Phenomics Research Center Nanjing Agricultural UniversityNanjing 210095China

High-quality rice reference genomes have accelerated the comprehensive identification of genome-wide variations and research on functional genomics and ***-you-hua-zhan has been a leading hybrid in China over the past ***,de novo genome assembly strategy optimization for the rice indica lines Huazhan(HZ)and Tianfeng(TF),including sequencing platforms,assembly pipelines and sequence depth,was carried *** PacBio and Nanopore platforms for long-read se-quencing were utilized,with the Canu,wtdbg2,SMARTdenovo,Flye,Canu-wtdbg2,Canu-SMARTdenovo and Canu-Flye *** combination of PacBio and Canu was optimal,considering the contig N50 length,contig number,assembled genome size and polishing *** assembled contigs were scaffolded with Hi-C data,resulting in two“golden quality”rice reference genomes,and evaluated using the scaffold N50,BUSCO,and LTR assembly ***,42,625 and 41,815 non-transposable element genes were annotated for HZ and TF,*** on our assembly of HZ and TF,as well as Zhenshan97,Minghui63,Shuhui498 and 9311,comprehensive variations were identified using Nipponbare as a *** de novo assembly strategy for rice we optimized and the“golden quality”rice genomes we produced for HZ and TF will benefit rice genomics and breeding research,especially with respect to uncovering the genomic basis of the elite traits of HZ and TF.

关键词： de novo genome assembly high-quality PacBio Nanopore variation rice

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