Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

第一作者：Noe Fernandez‐Pozo

第一单位：Stefan A. Rensing

通讯作者：马尔堡大学

 Abstract 

背景回顾：Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters.

提出问题：Its genome assembly was recently improved but the gene annotation was not updated.

主要研究：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 5,606 additional genes.

结果1-同源基因：Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, that could be partially explained by loss of homeologs derived from At‐α polyploidization event, and a lower occurrence of tandem duplications after divergence of Aethionemae from the other Brassicaceae.

结果2-MADS-box基因：Benchmarking of MADS‐ox genes identified orthologs of FUL and AGL79, not found in previous versions.

结果3-休眠：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 TUR and CYP ecotypes.

结论：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).

 摘 要 

阿拉伯岩芥（Aethionema arabicum）是十字花科性状演化，尤其是种子（发育、调控、萌发和休眠）以及果实（发育、开裂）等特性研究的模式植物。该物种的基因组最近有了更新，但是基因注释文件并未更新。本文中，作者利用294个RNA-seq和136307个全长PacBio Iso-Seq转录本对阿拉伯岩芥的基因注释进行了更新，提升了BUSCO评估约11.6%，新鉴定了5606个基因。同源基因分析显示与其他十字花科的植物相比，阿拉伯岩芥中的同源基因数量较低，这可能是At‐α多倍化事件之后的基因丢失所导致的；另外一方面，在Aethionemae与其他十字花科植物分化之后，串联重复出现的频率明显更低。通过MADS-box基因家族的鉴定，作者发现了FUL和AGL79在阿拉伯岩芥中的同源基因，这在之前的版本中是未曾鉴定得到的。通过对ABA介导的种子休眠全长转录组分析，作者发现了一个保守的PIF6‐β异构体和ABI3、ABI4以及DOG1的反义转录本，并且发现TUR和CYP生态型之间的不同可变剪切。本文所提供的数据有助于可变剪切的挖掘以及后续的功能和演化基因组学研究。作者还开发了一个在线数据库，方便研究人员在线获取阿拉伯岩芥的基因组和相关注释信息。

 通讯作者 

**Stefan A. Rensing**

doi: https://doi.org/10.1111/tpj.15161

Journal: the plant journal

Published date: Jan 16, 2021