Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.
Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.
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DOI：
10.3390/genes9040185
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发表时间：
2018-03-28
期刊：
影响因子：
3.5
通讯作者：
Brukhin V
中科院分区：
文献类型：
--
作者：
Kliver S;Rayko M;Komissarov A;Bakin E;Zhernakova D;Prasad K;Rushworth C;Baskar R;Smetanin D;Schmutz J;Rokhsar DS;Mitchell-Olds T;Grossniklaus U;Brukhin V
与模式植物拟南芥（Arabidopsis thaliana）密切相关的Boechera属已知包含有性和无生殖的物种或物种。逆戟鲸是一种有性繁殖的二倍体物种，被认为是无融合种的祖先亲本种。在这里，我们报道了利用来自1对末端和3对配对文库的短Illumina和Roche reads对逆转录双歧杆菌基因组进行从头组装。配对端文库中23-mers的分布表明其杂合性较低，存在可检测到的重复和重复。基因组大小估计为227 Mb，组装支架的N50为2.3 Mb。使用结合同源性和从头方法的混合方法，预测了27,048个蛋白质编码基因。此外，重复，转移RNA （tRNA）和核糖体RNA （rRNA）基因被注释。最后，利用芥蓝和其他6种芸苔科植物的基因进行系统发育树重建。此外，我们探索了与Boechera无融合相关的组氨酸外切酶APOLLO位点，并通过一系列重复提出了其进化模型。逆转录双歧杆菌的基因组组装将有助于高杂合性非杂交物种基因组的组装。
Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.
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影响因子：
16.8
作者：
Lee CR;Wang B;Mojica JP;Mandáková T;Prasad KVSK;Goicoechea JL;Perera N;Hellsten U;Hundley HN;Johnson J;Grimwood J;Barry K;Fairclough S;Jenkins JW;Yu Y;Kudrna D;Zhang J;Talag J;Golser W;Ghattas K;Schranz ME;Wing R;Lysak MA;Schmutz J;Rokhsar DS;Mitchell-Olds T
通讯作者：
Mitchell-Olds T
影响因子：
4.9
作者：
Bao W;Kojima KK;Kohany O
通讯作者：
Kohany O
DOI：
10.1093/bioinformatics/btv433
发表时间：
2015-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cheong WH;Tan YC;Yap SJ;Ng KP
通讯作者：
Ng KP
影响因子：
11.4
作者：
Anderson, Jill T.;Willis, John H.;Mitchell-Olds, Thomas
通讯作者：
Mitchell-Olds, Thomas
影响因子：
3
作者：
Aliyu, Olawale M.;Schranz, M. Eric;Sharbel, Timothy F.
通讯作者：
Sharbel, Timothy F.