Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.
Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.
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DOI：
10.1111/tpj.15161
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发表时间：
2021-04
期刊：
影响因子：
--
通讯作者：
Rensing SA
中科院分区：
文献类型：
--
作者：
Fernandez-Pozo N;Metz T;Chandler JO;Gramzow L;Mérai Z;Maumus F;Mittelsten Scheid O;Theißen G;Schranz ME;Leubner-Metzger G;Rensing SA
Aethionema arabicum是被子植物科性状进化的重要模式植物，特别是种子（发育、调节、萌发、休眠）和果实（发育、开裂机制）性状的进化。它的基因组组装最近得到了改进，但基因注释没有更新。在这里，我们改进了Ae。使用294个RNA-seq文库和136307个全长PacBio Iso-seq转录本进行阿拉伯树胶基因注释，将BUSCO完整性提高了11.6%，并具有5606个额外的基因。直向同源物的分析表明，在Ae中的基因数量较少。这可以部分地解释为来自At-α多倍化事件的同源物的丢失以及Aethionema从其他拟南芥科分化后串联重复的发生率较低。MADS盒基因的基准鉴定了在先前版本中未发现的FUL和AGL 79的直系同源物。对与阿坝介导的种子休眠相关的全长转录物的分析发现了PIF 6-β的保守同种型和ABI 3、ABI 4和DOG 1中的反义转录物，以及土耳其和塞浦路斯生态型之间发现的不同选择性剪接的其他情况。所呈现的数据允许选择性剪接挖掘和许多假说的命题，以研究进化和功能基因组学。注释数据和序列可在Ae. Arabicum DB（https：//plantcode.online.uni-marburg.de/aetar_db）。使用长读转录本测序改进的Aethionema arabicum基因注释提供了大量的全长同种型，为拟南芥科进化研究提供了重要资源。
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA‐seq libraries and 136 307 full‐length PacBio Iso‐seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At‐α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS‐box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full‐length transcripts related to ABA‐mediated seed dormancy discovered a conserved isoform of PIF6‐β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni‐marburg.de/aetar_db). Improved gene annotation of Aethionema arabicum using long‐read transcript sequencing provides a plethora of full‐length isoforms and an important resource for Brassicaceae evolution studies.
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影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
3.7
作者：
Cartolano M;Huettel B;Hartwig B;Reinhardt R;Schneeberger K
通讯作者：
Schneeberger K
大米中的MADS-box基因家族：在生殖发育和压力期间，全基因组识别，组织和表达分析。
影响因子：
4.4
作者：
Arora, Rita;Agarwal, Pinky;Ray, Swatismita;Singh, Ashok Kumar;Singh, Vijay Pal;Tyagi, Akhilesh K.;Kapoor, Sanjay
通讯作者：
Kapoor, Sanjay
影响因子：
5.6
作者：
Del Carmen Martínez-Ballesta M;Moreno DA;Carvajal M
通讯作者：
Carvajal M
影响因子：
4.4
作者：
Santamaría ME;Diaz-Mendoza M;Diaz I;Martinez M
通讯作者：
Martinez M