Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis1,212
Cloning and Sequencing of cDNAs for Hypothetical Genes from Chromosome 2 of Arabidopsis1,212
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拟南芥 2 号染色体假设基因 cDNA 的克隆和测序1,212
DOI：
10.1104/pp.010207
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发表时间：
2002
期刊：
影响因子：
7.4
通讯作者：
C. Town
中科院分区：
文献类型：
--
作者：
Yongli Xiao;M. Malik;C. Whitelaw;C. Town
在完全测序和注释的拟南芥基因组中，大约25%的基因具有仅由计算机算法预测的结构，而没有来自其他物种的核酸或蛋白质同源物的支持，或者来自拟南芥的表达序列匹配。这些被称为“假设基因”。在2号染色体上，由基因组研究所测序，在总共大约4100个基因中，大约有800个假设基因。为了测试它们在不同生长条件下和特定组织中的表达，我们使用了6个来自冷处理、热处理和病原菌(Xanthomonas Campestris PV Campestris)感染的植物、愈伤组织、根和幼苗的cDNA群体。到目前为止，已经测试了169个假设基因，其中138个基因被发现在六个cdna群体中的一个或多个中表达。通过对每个5‘和3’端快速扩增(RACE)产物的多个克隆进行测序和组装，我们获得了其中16个基因的全长序列。对于14个基因，有一个全长组装精确地支持其基因预测的内含子-外显子边界，只添加了5‘和3’非翻译区序列。然而，对于这些基因中的三个，其他组合代表额外的外显子，或者是剪接的或非剪接的内含子。对于剩下的两个基因，cdna序列显示与预测的基因结构有很大差异。此外，共有6个基因显示了一个以上的多聚腺苷酸化位点。这些数据将用于更新基因组研究所注释数据库ATH1中的基因模型。
About 25% of the genes in the fully sequenced and annotated Arabidopsis genome have structures that are predicted solely by computer algorithms with no support from either nucleic acid or protein homologs from other species or expressed sequence matches from Arabidopsis. These are referred to as “hypothetical genes.” On chromosome 2, sequenced by The Institute for Genomic Research, there are approximately 800 hypothetical genes among a total of approximately 4,100 genes. To test their expression under various growth conditions and in specific tissues, we used six cDNA populations prepared from cold-treated, heat-treated, and pathogen (Xanthomonas campestris pv campestris)-infected plants, callus, roots, and young seedlings. To date, 169 hypothetical genes were tested, and 138 of them are found to be expressed in one or more of the six cDNA populations. By sequencing multiple clones from each 5′- and 3′-rapid amplification of cDNA ends (RACE) product and assembling the sequences, we generated full-length sequences for 16 of these genes. For 14 genes, there was one full-length assembly that precisely supported the intron-exon boundaries of their gene predictions, adding only 5′- and 3′-untranslated region sequences. However, for three of these genes, the other assemblies represent additional exons and alternatively spliced or unspliced introns. For the remaining two genes, the cDNA sequences reveal major differences with predicted gene structures. In addition, a total of six genes displayed more than one polyadenylation site. These data will be used to update gene models in The Institute for Genomic Research annotation database ATH1.
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DOI：
10.1073/pnas.85.23.8998
发表时间：
1988-12-01
影响因子：
11.1
作者：
FROHMAN, MA;DUSH, MK;MARTIN, GR
通讯作者：
MARTIN, GR
影响因子：
14.9
作者：
Brendel, V;Kleffe, J
通讯作者：
Kleffe, J
影响因子：
4.4
作者：
Huang, XQ;Adams, MD;Kerlavage, AR
通讯作者：
Kerlavage, AR
影响因子：
5.6
作者：
Burge, C;Karlin, S
通讯作者：
Karlin, S