Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay.
Planta. 2022 Jul 27;256(3):50. doi: 10.1007/s00425-022-03961-9.
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
卫星 DNA 和长末端重复 (LTR) 反转录元件丰度的变化是导致二倍体花生属基因组大小和异染色质含量变化的主要因素。南美洲的花生属（豆科）包括 83 个种，分为九个分类群。其中，花生属 Arachis 组的特点是物种具有广泛的基因组和染色体多样性。这种多样性主要由重复 DNA 的数量和组成决定。在这里，我们对低覆盖度基因组测序进行了计算分析，以推断导致花生属二倍体（x=10）物种基因组分化的主要重复家族的变化动态，重点关注花生属 Arachis 组。估计的重复含量范围为基因组的 62.50%至 71.68%。基因组组成不同的物种往往具有不同的重复序列景观。Athila 家族反转录转座子是花生属重复组中最丰富和最具变异性的谱系，在物种进化的不同时期推断出转座活性的峰值。卫星 DNA（satDNA）的丰度较低，但在物种间的表现不同。富含 AT 的 satDNA 超家族的高进化率导致花生属基因组中异染色质的差异积累。基因组大小变化与重复含量之间的关系很复杂。然而，最大的基因组呈现出更高的 LTR 元件积累和更低的 satDNA 含量。相比之下，基因组最小的物种倾向于积累 satDNA，而牺牲 LTR 元件。基于重复 DNA 的系统发育分析支持花生属 Arachis 组的基因组排列。总之，我们的研究结果提供了最全面的重复组动态图片，这些图片导致了花生属物种的基因组分化。
