Data from: A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

BACKGROUND: MADS-box genes encode a family of eukaryotic transcription factors distinguished by the presence of a highly-conserved ~58 amino acid DNA-binding and dimerization domain (the MADS-box). The central role played by MADS-box genes in peach endodormancy regulation led us to examine this large gene family in more detail. We identified the locations and sequences of 79 MADS-box genes in peach, separated them into established subfamilies, and broadly surveyed their tissue-specific and dormancy-induced expression patterns using next-generation sequencing. We then focused on the dormancy-related SVP/AGL24 and FLC subfamilies, comparing their numbers and phylogenetic relationships with those of other sequenced woody perennial genomes. RESULTS: We identified 79 MADS-box genes distributed across all eight peach chromosomes and frequently located in clusters of two or more genes. They encode proteins with a mean length of 248 ± 72 amino acids and include representatives from most of the thirteen Type II (MIKC) subfamilies, as well as members of the Type I Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in species-specific monophyletic lineages, and their expression in the peach sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs and were expressed at much higher levels throughout vegetative and fruit tissues. During short-day-induced growth cessation, seven Type II genes from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes in expression. Phylogenetic analyses indicated that multiple, independent expansions have taken place within the SVP/AGL24 andFLC lineages in woody perennial species. CONCLUSIONS: Most Type I genes appear to have arisen through tandem duplications after the divergence of the Arabidopsis and peach lineages, whereas Type II genes appear to have increased following whole genome duplication events. An exception to the latter rule occurs in the FLC and SVP/AGL24 Type II subfamilies, in which species-specific tandem duplicates have been retained in a number of perennial species. These subfamilies comprise part of a genetic toolkit that regulates endodormancy transitions, but phylogenetic and expression data suggest that individual orthologs may not function identically across all species.

背景：MADS-box基因编码一类真核转录因子家族，其标志性特征是拥有一段高度保守的约58个氨基酸的DNA结合与二聚化结构域（MADS-box结构域）。鉴于MADS-box基因在桃内休眠调控中发挥核心作用，我们对该大型基因家族开展了更为深入的研究。我们在桃基因组中鉴定出79个MADS-box基因的位置与序列，将其划分为已确立的亚家族，并借助下一代测序技术（next-generation sequencing）全面分析了其组织特异性表达模式与休眠诱导表达模式。随后我们聚焦于休眠相关的SVP/AGL24与FLC亚家族（SVP/AGL24 and FLC subfamily），将其基因数量与系统发育关系与其他已测序木本多年生植物基因组进行了对比分析。
结果：我们在桃的全部8条染色体上鉴定出79个MADS-box基因，这些基因常以2个及以上成簇的形式分布。这些基因编码的蛋白质平均长度为248±72个氨基酸，涵盖了13个II型（MIKC）亚家族中的绝大多数成员，以及I型Mα、Mβ与Mγ亚家族的成员。绝大多数I型基因以物种特异性单系谱系的形式存在，且在桃孢子体中的表达量较低或几乎不表达。多数II型基因存在拟南芥直系同源基因，且在营养组织与果实组织中的表达量显著更高。在短日照诱导的生长停止过程中，来自SVP/AGL24、AGL17与SEP亚家族（AGL17 and SEP subfamily）的7个II型基因的表达量发生了显著变化。系统发育分析表明，在木本多年生植物的SVP/AGL24与FLC谱系中，发生了多起独立的基因扩张事件。
结论：绝大多数I型基因是在拟南芥与桃谱系分化后通过串联复制产生的，而II型基因的扩张则多源自全基因组复制事件。FLC与SVP/AGL24 II型亚家族属于该规律的例外：在多个多年生物种中，该亚家族保留了物种特异性的串联复制基因。这些亚家族构成了调控内休眠转变的遗传工具包的一部分，但系统发育与表达数据表明，不同物种中的直系同源基因的功能未必完全一致。