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基于双色高粱全长cDNA的转录本功能与表达分析

Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor.

作者信息

Shimada Setsuko, Makita Yuko, Kuriyama-Kondou Tomoko, Kawashima Mika, Mochizuki Yoshiki, Hirakawa Hideki, Sato Shusei, Toyoda Tetsuro, Matsui Minami

机构信息

Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.

RIKEN Advanced Center for Computing and Communication (ACCC), Wako, Saitama 351-0198, Japan.

出版信息

DNA Res. 2015 Dec;22(6):485-93. doi: 10.1093/dnares/dsv030. Epub 2015 Nov 5.

DOI:10.1093/dnares/dsv030
PMID:26546227
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4675717/
Abstract

Sorghum bicolor is one of the most important crops for food and bioethanol production. Its small diploid genome and resistance to environmental stress make sorghum an attractive model for studying the functional genomics of the Saccharinae and other C4 grasses. We analyzed the domain-based functional annotation of the cDNAs using the gene ontology (GO) categories for molecular function to characterize all the genes cloned in the full-length cDNA library of sorghum. The sorghum cDNA library successfully captured a wide range of cDNA-encoded proteins with various functions. To characterize the protein function of newly identified cDNAs, a search of their deduced domains and comparative analyses in the Oryza sativa and Zea mays genomes were carried out. Furthermore, genes on the sense strand corresponding to antisense transcripts were classified based on the GO of molecular function. To add more information about these genes, we have analyzed the expression profiles using RNA-Seq of three tissues (spikelet, seed and stem) during the starch-filling phase. We performed functional analysis of tissue-specific genes and expression analysis of genes of starch biosynthesis enzymes. This functional analysis of sorghum full-length cDNAs and the transcriptome information will facilitate further analysis of the Saccharinae and grass families.

摘要

高粱是粮食和生物乙醇生产最重要的作物之一。其小的二倍体基因组和对环境胁迫的抗性使高粱成为研究甘蔗亚族和其他C4禾本科植物功能基因组学的有吸引力的模型。我们使用分子功能的基因本体（GO）类别分析了cDNA基于结构域的功能注释，以表征高粱全长cDNA文库中克隆的所有基因。高粱cDNA文库成功捕获了具有各种功能的广泛的cDNA编码蛋白。为了表征新鉴定的cDNA的蛋白质功能，对其推导的结构域进行了搜索，并在水稻和玉米基因组中进行了比较分析。此外，根据分子功能的GO对与反义转录本对应的有义链上的基因进行了分类。为了添加有关这些基因的更多信息，我们使用RNA-Seq分析了淀粉填充阶段三个组织（小穗、种子和茎）的表达谱。我们对组织特异性基因进行了功能分析，并对淀粉生物合成酶的基因进行了表达分析。高粱全长cDNA的这种功能分析和转录组信息将有助于对甘蔗亚族和禾本科进行进一步分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7a26879a678b/dsv03006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/5b55a4049bef/dsv03001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/0f3a9dafabb9/dsv03002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/8a7000f6e29e/dsv03003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7a30e843a5e9/dsv03004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7f6f2bf6fbb7/dsv03005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7a26879a678b/dsv03006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/5b55a4049bef/dsv03001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/0f3a9dafabb9/dsv03002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/8a7000f6e29e/dsv03003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7a30e843a5e9/dsv03004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7f6f2bf6fbb7/dsv03005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b064/4675717/7a26879a678b/dsv03006.jpg

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Plant Physiol. 2014 Sep;166(1):252-64. doi: 10.1104/pp.114.240689. Epub 2014 Jul 18.
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Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress.高粱响应复合热干旱胁迫的转录组分析。
BMC Genomics. 2014 Jun 10;15(1):456. doi: 10.1186/1471-2164-15-456.
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Microarray analysis of differentially expressed mRNAs and miRNAs in young leaves of sorghum under dry-down conditions.干旱条件下高粱幼叶中差异表达的mRNA和miRNA的微阵列分析
J Plant Physiol. 2014 Apr 15;171(7):537-48. doi: 10.1016/j.jplph.2013.12.014. Epub 2014 Mar 13.
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Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling.通过全基因组转录组分析鉴定具有不同氮胁迫耐受性的高粱基因型之间的差异表达基因。
BMC Genomics. 2014 Mar 5;15:179. doi: 10.1186/1471-2164-15-179.
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A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums.高粱表达图谱揭示了粮食、甜高粱和生物能源高粱营养组织中基因型特异性表达的动态变化。
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