The availability of a large number of whole-genome sequences allows comparative genomic analysis to reveal and understand evolution of regulatory regions and elements. The role played by events such as whole-genome and segmental duplications followed by genome fractionation in shaping genomic landscape and in expansion of gene families is crucial toward developing insights into evolutionary trends and consequences such as sequence and functional diversification. Members of Brassicaceae are known to have experienced several rounds of whole-genome duplication (WGD) that have been termed as paleopolyploidy, mesopolyploidy, and neopolyploidy. Such repeated events led to the creation and expansion of a large number of gene families. MIR319 is reported to be one of the most ancient and conserved plant MIRNA families and plays a role in growth and development including leaf development, seedling development, and embryo patterning. We have previously reported functional diversification of members of miR319 in Brassica oleracea affecting leaf architecture; however, the evolutionary history of the MIR319 gene family across Brassicaceae remains unknown and requires investigation. We therefore identified homologous and homeologous segments of ca. 100 kb, with or without MIR319, performed comparative synteny analysis and genome fractionation studies. We detected variable rates of gene retention across members of Brassicaceae when genomic blocks of MIR319a, MIR319b, and MIR319c were compared either between themselves or against Arabidopsis thaliana genome which was taken as the base genome. The highest levels of shared genes were found between A. thaliana and Capsella rubella in both MIR319b- and MIR319c-containing genomic segments, and with the closest species of A. thaliana, A. lyrata, only in MIR319a-containing segment. Synteny analysis across 12 genomes (with 30 sub-genomes) revealed MIR319c to be the most conserved MIRNA loci (present in 27 genomes/sub-genomes) followed by MIR319a (present in 23 genomes/sub-genomes); MIR319b was found to be frequently lost (present in 20 genomes/sub-genomes) and thus is under least selection pressure for retention. Genome fractionation revealed extensive and differential loss of MIRNA homeologous loci and flanking genes from various sub-genomes of Brassica species that is in accordance with their older history of polyploidy when compared to Camelina sativa, a recent neopolyploid, where the effect of genome fractionation was least. Finally, estimation of phylogenetic relationship using precursor sequences of MIR319 reveals MIR319a and MIR319b form sister clades, with MIR319c forming a separate clade. An intra-species synteny analysis between MIR319a-, MIR319b-, and MIR319c-containing genomic segments suggests segmental duplications at the base of Brassicaceae to be responsible for the origin of MIR319a and MIR319b.

中文翻译：

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微同步分析，以了解十字花科植物芸苔科中MIR319家族的进化和影响。

大量全基因组序列的可用性允许进行比较基因组分析，以揭示和了解调控区和元件的进化。诸如全基因组和节段重复的事件，继之以基因组分级在塑造基因组景观和基因家族扩展中所起的作用，对于深入了解进化趋势和后果（例如序列和功能多样化）至关重要。已知十字花科的成员经历了数轮全基因组复制（WGD），这些重复被称为古多倍体，中多倍体和新多倍体。此类重复事件导致大量基因家族的建立和扩展。MIR319据报道，它是最古老和最保守的植物MIRNA家族之一，在包括叶片发育，幼苗发育和胚模式形成在内的生长和发育中发挥着作用。我们先前已经报道了甘蓝型油菜中miR319成员的功能多样化，影响了叶片的结构。但是，整个十字花科的MIR319基因家族的进化历史仍然未知，需要进一步研究。因此，我们确定了ca的同源和同源片段。有或没有MIR319的100 kb都进行了比较同义分析和基因组分离研究。当我们的基因组块将它们之间或与拟南芥拟南芥基因组之间的MIR319a，MIR319b和MIR319c进行比较，该基因组被视为基础基因组。最高级别的小号共有的基因被发现之间拟南芥和荠菜风疹在两个MIR319b -和MIR319c含基因组片段，并与最近的种拟南芥，A.胡菜，仅在MIR319a含段。对12个基因组（包含30个亚基因组）的同义分析显示MIR319c是最保守的MIRNA位点（存在于27个基因组/亚基因组中），其次是MIR319a（存在于23个基因组/亚基因组中）；MIR319b被发现经常丢失（存在于20个基因组/亚基因组中），因此保留的选择压力最小。基因组分级显示与芸苔属（Camelina sativa）相比，芸苔属各亚基因组的MIRNA同源基因座和侧翼基因广泛而差异性丢失，这与它们较早的多倍性历史相符，而最近的新多倍体中基因组分级的影响最小。最后，使用MIR319的前体序列估算系统发育关系可揭示MIR319a和MIR319b形成姐妹进化枝，而MIR319c形成单独的进化枝。包含MIR319a-，MIR319b-和MIR319c的基因片段之间的种内同义分析表明，十字花科底部的节段重复是MIR319a和MIR319b起源的原因。