Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth

First author: Jasmien Vercruysse; Affiliations: Ghent University (根特大学): Gent, Belgium

Corresponding author: Dirk Inzé

Leaf growth is a complex trait for which many similarities exist in different plant species, suggesting functional conservation of the underlying pathways. However, a global view of orthologous genes involved in leaf growth showing conserved expression in dicots and monocots is currently missing. Here we present a genome‐wide comparative transcriptomics analysis between Arabidopsis and maize, identifying conserved biological processes and gene functions active during leaf growth. Despite the orthology complexity between these distantly related plants, 926 orthologous gene groups including 2,829 Arabidopsis and 2,974 maize genes with similar expression during leaf growth were found, indicating conservation of the underlying molecular networks. We found 65% of these genes involved in one‐to‐one orthology, whereas only 28.7% of the groups with divergent expression had one‐to‐one orthology. Within the pool of genes with conserved expression, 19 transcription factor families were identified, demonstrating expression conservation of regulators active during leaf growth. Additionally, 25 Arabidopsis and 25 maize putative targets of the TCP TFs with conserved expression were determined based on the presence of enriched transcription factor binding sites. Based on large‐scale phenotypic data, we observed that genes with conserved expression have a higher probability to be involved in leaf growth and that leaf‐related phenotypes are more frequently present for genes having orthologs between dicots and monocots than clade‐specific genes. This study shows the power of integrating transcriptomics with orthology data to identify or select candidates for functional studies during leaf development in flowering plants.

叶片生长是一个复杂的性状，不同的植物物种在叶片生长方面存在着许多的相似性，说明必定存在着一些功能保守。然而，目前整个基因组范围上单、双子叶物种叶片生长时具有保守表达模式的同源基因还不清楚。本文中，作者比较了拟南芥和玉米的叶片生长转录组，鉴定了一些保守的生物学进程以及基因功能。尽管拟南芥和玉米的亲缘关系较远，作者仍鉴定到了926对同源基因，包括2829个拟南芥和2974个玉米基因在叶片发育过程中有着相似的表达模式，说明拟南芥和玉米在叶片生长潜在分子调控网络方面的确存在一定的保守性。作者发现这些同源基因中，大约有65%的基因是1:1的同源关系，而那些具有不同表达模式的同源基因中仅有28.7%的属于1:1的同源关系。在具有保守表达模式的基因中，作者鉴定了19个转录因子家族，说明这两个物种叶片生长过程中具有保守的调控激活过程。另外，作者通过判断基因上是否富集转录因子结合位点，发现TCP转录因子在拟南芥和玉米中有25个靶基因存在类似的表达模式。基于大规模的表型数据，作者观察到具有保守表达模式的基因往往参与叶片生长的可能性更高，并且相比于拟南芥和玉米物种特异性基因，在这两个物种中都具有的同源基因往往更加容易出现叶片相关的表型。本文的研究显示通过整合转录组学和同源基因数据来鉴定或选择有花植物叶片发育过程功能研究的候选基因是可行的。

通讯：Dirk Inzé (http://www.vib.be/en/research/scientists/Pages/Dirk-Inze-Lab.aspx)

个人简介：1984年，根特大学，博士。

研究方向：植物叶片生长以及控制植物叶片最终大小的分子机制。

doi: https://doi.org/10.1111/pbi.13223

Journal: Plant Biotechnology Journal

First Published: July 30, 2019