İnal Behcet, Büyük İlker, İlhan Emre, Aras Sümer
Department of Agricultural Biotechnology, Faculty of Agriculture, Siirt University, Siirt, Turkey.
Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey.
3 Biotech. 2017 Oct;7(5):302. doi: 10.1007/s13205-017-0933-0. Epub 2017 Sep 8.
The aim of this study was to identify and characterize the - family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight genes were detected. These segmentally duplicated gene couples were -/-, -/- and -/-. The predicted number of exons among the genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. -, -, - and - genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for - and - after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue- and cultivar-specific expression patterns.
本研究的目的是在菜豆中通过全基因组规模鉴定并表征YABBY基因家族。研究采用了多种电子生物学方法，并通过常规分子生物学技术对结果进行了验证。在盐胁迫条件下，对两个菜豆品种Yakutiye和Zulbiye的叶片和根组织中已鉴定的假定YABBY基因进行了定量实时PCR（qPCR）分析。发现了8个候选PvulYABBY蛋白，这些蛋白的长度在173至256个氨基酸之间。YABBY蛋白的等电点（pI）在5.18至9.34之间，从酸性到碱性不等，PvulYABBYs的分子量在18978.4至28916.8 Da之间。在已鉴定的8个YABBY基因中检测到3对片段重复基因对。这些片段重复基因对分别是PvulYABBY1/PvulYABBY2、PvulYABBY3/PvulYABBY4和PvulYABBY5/PvulYABBY6。YABBY基因中预测的外显子数量从6个到8个外显子不等。此外，所有发现的基因在开放阅读框（ORF）内都包含内含子。PvulYABBY1、PvulYABBY2、PvulYABBY3和PvulYABBY4基因被5种植物的miRNA靶向，共检测到5个miRNA家族（miR5660、miR1157、miR5769、miR5286和miR8120）。根据RNA测序分析，在菜豆的叶片和根组织中，除PvulYABBY5和PvulYABBY6外，所有基因在盐胁迫处理后均上调或下调。根据qPCR分析，8个基因中有6个在叶片中表达，但8个基因中只有4个在根中表达，并且这些基因表现出组织和品种特异性的表达模式。
