Castro Natália, Vilela Bruno, Mata-Sucre Yennifer, Marques André, Gagnon Edeline, Lewis Gwilym P, Costa Lucas, Souza Gustavo
Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Center, Federal University of Pernambuco, Recife, Brazil.
Institute of Biology, Federal University of Bahia, Salvador, Bahia, Brazil.
Mol Ecol. 2024 Sep 9:e17510. doi: 10.1111/mec.17510.
Fluctuations in genomic repetitive fractions (repeatome) are known to impact several facets of evolution, such as ecological adaptation and speciation processes. Therefore, investigating the divergence of repetitive elements can provide insights into an important evolutionary force. However, it is not clear how the different repetitive element clades are impacted by the different factors such as ecological changes and/or phylogeny. To discuss this, we used the Neotropical legume genus Erythrostemon (Caesalpinioideae) as a model, given its ancient origin (~33 Mya), lineage-specific niche conservatism, macroecological heterogeneity, and disjunct distribution in Meso- and South American (MA and SA respectively) lineages. We performed a comparative repeatomic analysis of 18 Erythrostemon species to test the impact of environmental variables over repeats diversification. Overall, repeatome composition was diverse, with high abundances of satDNAs and Ty3/gypsy-Tekay transposable elements, predominantly in the MA and SA lineages respectively. However, unexpected repeatome profiles unrelated to the phylogeny/biogeography were found in a few MA (E. coccineus, E. pannosus and E. placidus) and SA (E. calycinus) species, related to reticulate evolution and incongruence between nuclear and plastid topology, suggesting ancient hybridizations. The plesiomorphic Tekay and satDNA pattern was altered in the MA-sensu stricto subclade with a striking genomic differentiation (expansion of satDNA and retraction of Tekay) associated with the colonization of a new environment in Central America around 20 Mya. Our data reveal that the current species-specific Tekay pool was the result of two bursts of amplification probably in the Miocene, with distinct patterns for the MA and SA repeatomes. This suggests a strong role of the Tekay elements as modulators of the genome-environment interaction in Erythrostemon, providing macroevolutionary insights about mechanisms of repeatome differentiation and plant diversification across space and time.
基因组重复片段（重复组）的波动会影响进化的多个方面，如生态适应和物种形成过程。因此，研究重复元件的差异可以为一种重要的进化力量提供见解。然而，目前尚不清楚不同的重复元件分支如何受到生态变化和/或系统发育等不同因素的影响。为了探讨这一问题，我们以新热带豆科植物刺桐属（苏木亚科）为模型，考虑到其古老的起源（约3300万年前）、谱系特异性的生态位保守性、宏观生态异质性以及在中美洲和南美洲（分别为MA和SA）谱系中的间断分布。我们对18种刺桐属植物进行了比较重复组分析，以测试环境变量对重复序列多样化的影响。总体而言，重复组组成多样，卫星DNA和Ty3/gypsy-Tekay转座元件丰度较高，分别主要存在于MA和SA谱系中。然而，在一些MA（刺桐、绒毛刺桐和平滑刺桐）和SA（萼花刺桐）物种中发现了与系统发育/生物地理学无关的意外重复组图谱，这与网状进化以及核拓扑和质体拓扑之间的不一致有关，表明存在古老的杂交现象。在MA狭义亚分支中，原始的Tekay和卫星DNA模式发生了改变，伴随着大约2000万年前在中美洲新环境定殖相关的显著基因组分化（卫星DNA的扩张和Tekay的收缩）。我们的数据表明，当前物种特异性的Tekay库可能是中新世两次扩增爆发的结果，MA和SA重复组具有不同的模式。这表明Tekay元件在刺桐属基因组-环境相互作用的调节中发挥了重要作用，为重复组分化和植物跨时空多样化的机制提供了宏观进化见解。
