Bhide Amey, Schliesky Simon, Reich Marlis, Weber Andreas P M, Becker Annette
Justus-Liebig-Universität Gießen, Institute of Botany, Plant Development Group, Heinrich-Buff-Ring 38, 35392 Gießen, Germany.
BMC Genomics. 2014 Feb 19;15:140. doi: 10.1186/1471-2164-15-140.
Arabidopsis thaliana, a member of the Brassicaceae family is the dominant genetic model plant. However, while the flowers within the Brassicaceae members are rather uniform, mainly radially symmetrical, mostly white with fixed organ numbers, species within the Cleomaceae, the sister family to the Brassicaceae show a more variable floral morphology. We were interested in understanding the molecular basis for these morphological differences. To this end, the floral transcriptome of a hybrid Tarenaya hassleriana, a Cleomaceae with monosymmetric, bright purple flowers was sequenced, annotated and analyzed in respect to floral regulators.
We obtained a comprehensive floral transcriptome with high depth and coverage close to saturation analyzed using rarefaction analysis a method well known in biodiversity studies. Gene expression was analyzed by calculating reads per kilobase gene model per million reads (RPKM) and for selected genes in silico expression data was corroborated by qRT-PCR analysis. Candidate transcription factors were identified based on differences in expression pattern between A. thaliana and T. hassleriana, which are likely key regulators of the T. hassleriana specific floral characters such as coloration and male sterility in the hybrid plant used. Analysis of lineage specific genes was carried out with members of the fabids and malvids.
The floral transcriptome of T. hassleriana provides insights into key pathways involved in the regulation of late anthocyanin biosynthesis, male fertility, flowering time and organ growth regulation which are unique traits compared the model organism A. thaliana. Analysis of lineage specific genes carried out with members of the fabids and malvids suggests an extensive gene birth rate in the lineage leading to core Brassicales while only few genes were potentially lost during core Brassicales evolution, which possibly reflects the result of the At-β whole genome duplication. Our analysis should facilitate further analyses into the molecular mechanisms of floral morphogenesis and pigmentation and the mechanisms underlying the rather diverse floral morphologies in the Cleomaceae.
拟南芥是十字花科的一员，是主要的遗传模式植物。然而，十字花科成员的花朵相当一致，主要为辐射对称，大多为白色且器官数量固定，而十字花科的姐妹科白花菜科的物种则表现出更多样化的花形态。我们有兴趣了解这些形态差异的分子基础。为此，对具有单对称、亮紫色花朵的白花菜科杂交种哈氏辣木的花转录组进行了测序、注释，并对花调控因子进行了分析。
我们获得了一个深度高且覆盖度接近饱和的综合花转录组，使用在生物多样性研究中熟知的稀疏分析方法进行分析。通过计算每百万读取中每千碱基基因模型的读取数（RPKM）来分析基因表达，并且对于选定的基因，通过qRT-PCR分析在计算机上证实了表达数据。基于拟南芥和哈氏辣木之间表达模式的差异鉴定了候选转录因子，这些差异可能是哈氏辣木特定花特征（如杂交植物中的着色和雄性不育）的关键调节因子。用豆类和锦葵类的成员进行了谱系特异性基因的分析。
哈氏辣木的花转录组为参与晚期花青素生物合成、雄性育性、开花时间和器官生长调控的关键途径提供了见解，这些是与模式生物拟南芥相比的独特特征。用豆类和锦葵类的成员进行的谱系特异性基因分析表明，在导致核心十字花目植物的谱系中基因出生率很高，而在核心十字花目植物进化过程中可能仅丢失了少数基因，这可能反映了At-β全基因组加倍的结果。我们的分析应有助于进一步分析花形态发生和色素沉着的分子机制以及白花菜科中相当多样的花形态的潜在机制。
