Sharma Akanksha, Sharma Niharika, Bhalla Prem, Singh Mohan
Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Melbourne, VIC, Australia.
Australian Centre for Plant Functional Genomics (ACPFG), School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Plant Genomics Centre, Hartley Grove, Urrbrae, SA, Australia.
PLoS One. 2017 Jan 19;12(1):e0169686. doi: 10.1371/journal.pone.0169686. eCollection 2017.
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional characterization in related grass species.
比较基因组学通过检测与亲缘关系较近或较远物种的基因组之间的异同，促进了从基因组序列中挖掘生物信息。通过使用这种比较方法，可以将知识从模式生物转移到非模式生物，并深入了解特定基因的结构和进化模式。由于缺乏致敏草的测序基因组，本研究旨在利用与致敏草具有系统发育关系的短柄草的基因组数据，了解草花粉过敏原的结构、组织和表达谱。将基因组数据与花药RNA测序数据集相结合，揭示了短柄草中属于8个过敏原组的24个花粉过敏原基因，这些基因定位在5条染色体上。在短柄草中，观察到24个已鉴定的假定过敏原编码基因具有高水平的花药特异性表达谱。基因组证据表明，编码5组过敏原的基因是花粉特异性孤儿基因，该过敏原是花粉症和过敏性哮喘的最主要诱因，起源于短柄草和小麦分支的常见草类祖先。基因结构分析表明，短柄草中假定的过敏原编码基因要么没有内含子，要么内含子数量减少。对已鉴定的短柄草基因的启动子分析表明，存在可能负责花药/花粉特异性高表达的特定顺式调控序列。通过在短柄草中鉴定假定的过敏原编码基因，本研究还首次在模式植物短柄草中描述了一些重要的植物基因家族（如扩展蛋白超家族、EF-手家族、肌动蛋白结合蛋白等）。总之，本研究为花粉过敏原的结构特征和进化提供了新的见解，并将进一步为相关草种中花粉过敏原的功能特征研究奠定基础。
