Table10.DOCX

Members of the YABBY gene family, a small plant-specific family of genes, have been proposed to function in specifying abaxial cell fate. Although to date little has been learned about cotton YABBY genes, completion of the cotton genome enables a comprehensive genome-wide analysis of YABBY genes in cotton. Here, a total of 12, 12, and 23 YABBY genes were identified in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G. hirsutum (2n = 4x = 52, [AD]t), respectively. Sequence analysis showed that the N-terminal zinc-finger and C-terminal YABBY domains in YABBY proteins are highly conserved among cotton, Arabidopsis, and rice. Eighty-five genes from eight sequenced species naturally clustered into five groups, and the YAB2-like group could be divided into three sub-groups, indicating that YABBYs are highly conserved among the examined species. Orthologs from the At and Dt sub-genomes (where “t” indicates tetraploid) showed good collinearity, indicating that YABBY loci are highly conserved between these two sub-genomes. Whole-genome duplication was the primary cause of upland cotton YABBY gene expansion, segmental duplication played important roles in YABBY gene expansion within the At and Dt sub-genomes, and the YAB5-like group was mainly generated by segmental duplication. The long-terminal repeat retroelements Copia and Gypsy were identified as major transposable elements accompanying the appearance of duplicated YABBY genes, suggesting that transposable element expansion might be involved in gene duplication. Selection pressure analyses using PAML revealed that relaxed purifying selection might be the main impetus during evolution of YABBY genes in the examined species. Furthermore, exon/intron pattern and motif analyses indicated that genes within the same group were significantly conserved between Arabidopsis and cotton. In addition, the expression patterns in different tissues suggest that YABBY proteins may play roles in ovule development because YABBYs are highly expressed in ovules. The expression pattern of YABBY genes showed that approximately half of the YABBYs were down-regulated under different stress treatments. Collectively, our results represent a comprehensive genome-wide study of the YABBY gene family, which should be helpful in further detailed studies on the gene function and evolution of YABBY genes in cotton.

YABBY基因家族（YABBY gene family）是一类小型植物特异性基因家族，其成员被认为参与远轴细胞命运的特化。尽管目前对棉花YABBY基因的了解甚少，但棉花基因组的完成使得我们能够对棉花YABBY基因开展全基因组范围的综合分析。本研究分别在亚洲棉（Gossypium arboreum，2n=26，A2）、雷蒙德氏棉（G. raimondii，2n=26，D5）和陆地棉（G. hirsutum，2n=4x=52，[AD]t）中鉴定出12、12和23个YABBY基因。序列分析表明，棉花、拟南芥和水稻的YABBY蛋白的N端锌指结构域与C端YABBY结构域均具有高度保守性。来自8个已测序物种的85个基因自然聚类为5个类群，其中YAB2类群可进一步划分为3个亚群，这表明在所分析的物种中YABBY基因家族具有高度保守性。来自At和Dt亚基因组（其中“t”代表异源四倍体）的直系同源基因表现出良好的共线性，说明这两个亚基因组之间的YABBY基因座高度保守。全基因组复制是陆地棉YABBY基因家族扩张的主要原因，片段复制在At和Dt亚基因组的YABBY基因扩张中发挥了重要作用，而YAB5类群主要由片段复制产生。研究发现长末端重复反转录转座子Copia和Gypsy是伴随YABBY基因复制事件出现的主要转座因子，这提示转座因子扩张可能参与了基因复制过程。使用PAML进行的选择压力分析显示，宽松纯化选择可能是所分析物种YABBY基因进化的主要推动力。此外，外显子-内含子结构与基序分析表明，拟南芥与棉花中同一类群的基因具有显著的保守性。另外，不同组织的表达模式分析提示，YABBY蛋白可能在胚珠发育中发挥作用，因为YABBY基因在胚珠中呈高表达。YABBY基因的表达谱显示，约半数的YABBY基因在不同胁迫处理下呈现下调表达趋势。综上，本研究代表了对YABBY基因家族的一项全面的全基因组研究，其结果将为后续棉花YABBY基因的功能与进化研究提供重要参考。