De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock.
De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock.
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DOI：
10.1111/tpj.12267
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发表时间：
2013-09
期刊：
影响因子：
--
通讯作者：
Marks MD
中科院分区：
文献类型：
--
作者：
Dorn KM;Fankhauser JD;Wyse DL;Marks MD
小蓟（Thlaspi arvense L.）具有作为油籽作物的潜力，可在美国中西部的秋季和冬季种植，并在早春收获作为生物柴油原料。通过传统的育种方法，一点也没有在农艺上对一点芥进行改良。基因组技术的最新进展允许开发基因组工具，以通过基因组辅助育种实现快速改进。在这里，我们报告了一个注释的转录组组装的一分钱。从代表性的植物组织中分离RNA，并产生2.03亿个独特的Illumina RNA-seq读数并用于转录组组装。转录组装配草图由33 873个重叠群组成，平均长度为1242 bp。一个全球性的比较之间的同源性的pennycress和拟南芥转录组，沿着与其他四个拟南芥科物种，揭示了高水平的全球序列保守的家庭。最后的组装功能注释，允许控制重要的农艺性状，如开花和硫苷代谢的推定基因的鉴定。这些基因的鉴定导致可测试的假设，其保守的功能和合理的策略，以改善在彭尼克雷斯农艺性状。未来的工作，以表征异构体之间的差异不同的pennycress线，并制定一个草案的基因组序列的pennycress将进一步指导性状的改善。
Field pennycress (Thlaspi arvense L.) has potential as an oilseed crop that may be grown during fall (autumn) and winter months in the Midwestern United States and harvested in the early spring as a biodiesel feedstock. There has been little agronomic improvement in pennycress through traditional breeding. Recent advances in genomic technologies allow for the development of genomic tools to enable rapid improvements to be made through genomic assisted breeding. Here we report an annotated transcriptome assembly for pennycress. RNA was isolated from representative plant tissues, and 203 million unique Illumina RNA-seq reads were produced and used in the transcriptome assembly. The draft transcriptome assembly consists of 33 873 contigs with a mean length of 1242 bp. A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family. The final assembly was functionally annotated, allowing for the identification of putative genes controlling important agronomic traits such as flowering and glucosinolate metabolism. Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress. Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.
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影响因子：
9.4
作者：
Hammond, JP;Bowen, HC;Broadley, MR
通讯作者：
Broadley, MR
耕作：功能基因组学的快捷方式。
影响因子：
2.4
作者：
Kurowska, Marzena;Daszkowska-Golec, Agata;Gruszka, Damian;Marzec, Marek;Szurman, Miriam;Szarejko, Iwona;Maluszynski, Miroslaw
通讯作者：
Maluszynski, Miroslaw
影响因子：
56.9
作者：
Johanson, U;West, J;Dean, C
通讯作者：
Dean, C
影响因子：
56.9
作者：
Fargione, Joseph;Hill, Jason;Hawthorne, Peter
通讯作者：
Hawthorne, Peter
DOI：
10.1073/pnas.0909766107
发表时间：
2010-10-26
影响因子：
11.1
作者：
Beilstein, Mark A.;Nagalingum, Nathalie S.;Mathews, Sarah
通讯作者：
Mathews, Sarah