Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response.
Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response.
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DOI：
10.1186/1471-2229-7-66
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发表时间：
2007-12-20
影响因子：
5.3
通讯作者：
Ishitani M
中科院分区：
文献类型：
--
作者：
Sakurai T;Plata G;Rodríguez-Zapata F;Seki M;Salcedo A;Toyoda A;Ishiwata A;Tohme J;Sakaki Y;Shinozaki K;Ishitani M
木薯是一种异源四倍体植物，它对非生物胁迫具有显著的耐受性，是人类和动物的重要能源，也是许多工业生产的原料。建立了木薯植株在正常、高温、干旱、铝胁迫和收获后生理劣变条件下的全长cDNA文库;利用表达序列标签（EST）对19968个克隆进行了序列特征分析。ESTs被组装成6355个重叠群和9026个单例，这些单例被进一步分组为10577个支架;我们发现了4621个新的木薯序列和1521个与植物蛋白质数据库没有显着相似性的序列。捕获了7796个不同基因的转录本，我们能够对其中78%的基因进行功能分类，同时发现超过一半的酶在拟南芥的代谢途径中进行了注释。未与其他物种的转录本配对的序列的注释包括许多与压力相关的功能类别，这表明我们的文库富含压力诱导的基因。最后，我们检测到230个假定的基因重复，包括活性氧信号通路中的关键酶，并可能在木薯胁迫反应特征中发挥作用。木薯全长cDNA文库包含参与应激反应的基因的转录本，以及木薯研究的不同领域的重要基因。该文库将成为基因发现、表征和克隆的重要资源;在不久的将来，它将有助于木薯基因组的注释。
Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs). The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome.
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影响因子：
5.8
作者：
Barker, G;Batley, J;Edwards, D
通讯作者：
Edwards, D
影响因子：
1.9
作者：
Cortés, DF;Reilly, K;Tohme, J
通讯作者：
Tohme, J
影响因子：
56.9
作者：
COCK, JH
通讯作者：
COCK, JH
影响因子：
4.9
作者：
ELSHARKAWY, MA;COCK, JH
通讯作者：
COCK, JH
影响因子：
1.6
作者：
El-Sharkawy, MA;Cadavid, LE
通讯作者：
Cadavid, LE