De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).
De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).
复制标题
DOI：
10.1186/1471-2164-12-30
复制
发表时间：
2011-01-13
期刊：
影响因子：
4.4
通讯作者：
Penin AA
中科院分区：
文献类型：
--
作者：
Logacheva MD;Kasianov AS;Vinogradov DV;Samigullin TH;Gelfand MS;Makeev VJ;Penin AA
转录组测序数据已成为现代遗传学、基因组学和进化生物学不可或缺的组成部分。然而，尽管DNA测序技术有所进步，但许多生物类群，尤其是许多植物类群，仍缺乏此类数据。在此，我们展示了两种近缘植物物种转录组测序的结果。这两个物种，荞麦（Fagopyrum esculentum）和苦荞麦（F. tataricum），属于石竹目——一大类进化关系不确定的开花植物。荞麦（普通荞麦）也是一种重要的粮食作物。尽管有这些实际和进化方面的考虑因素，但荞麦属物种尚未成为大规模测序项目的对象。
使用454焦磷酸测序技术对荞麦和苦荞麦花及花序中表达的基因所对应的标准化cDNA进行了测序。这产生了26.7万条（荞麦）和22.9万条（苦荞麦）读段，平均长度为341 - 349个核苷酸。对读段进行从头组装，每个物种产生了约2.5万个重叠群，覆盖度为7.5 - 8.2倍。对两个转录组的比较分析表明它们总体相似，但也揭示了可能差异表达的基因。其中包括反转录转座子基因以及参与糖生物合成和代谢的基因。13个单拷贝基因被用于系统发育分析；所得的系统发育树与从多基因质体数据集推断出的结果大体一致。石竹目和菊类植物的姐妹群关系现在从核基因序列中得到了有力支持。
对两种同属的开花植物物种，荞麦和苦荞麦，进行了454转录组测序和从头组装。结果产生了大量代表已知植物基因直系同源物以及潜在新基因的cDNA序列。
Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, Fagopyrum esculentum and F. tataricum, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. F. esculentum (common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects. Normalized cDNA corresponding to genes expressed in flowers and inflorescences of F. esculentum and F. tataricum was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for F. esculentum) and 229 (F. tataricum) thousands of reads with average length of 341-349 nucleotides. De novo assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences. 454 transcriptome sequencing and de novo assembly was performed for two congeneric flowering plant species, F. esculentum and F. tataricum. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.
登录
查看更多内容
影响因子：
5.3
作者：
Albert VA;Soltis DE;Carlson JE;Farmerie WG;Wall PK;Ilut DC;Solow TM;Mueller LA;Landherr LL;Hu Y;Buzgo M;Kim S;Yoo MJ;Frohlich MW;Perl-Treves R;Schlarbaum SE;Bliss BJ;Zhang X;Tanksley SD;Oppenheimer DG;Soltis PS;Ma H;DePamphilis CW;Leebens-Mack JH
通讯作者：
Leebens-Mack JH
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
3.4
作者：
Duarte, Jill M.;Wall, P. Kerr;dePamphilis, Claude W.
通讯作者：
dePamphilis, Claude W.
影响因子：
6.5
作者：
Licen, M;Kreft, I
通讯作者：
Kreft, I
影响因子：
2.3
作者：
Brockington, Samuel F.;Alexandre, Roolse;Soltis, Pamela S.
通讯作者：
Soltis, Pamela S.