Main conclusionWe demonstrated by cytogenomic analysis that the proximal heterochromatin of the Northeast Brazilian species of Caesalpinia group is enriched with phylogenetically conserved Ty3/Gypsy-Tekay RT, but diverge in the presence of Ty3/Gypsy-Athila RT and satDNA.AbstractThe Caesalpinia Group includes 225 species and 27 monophyletic genera of which four occur in Northeastern Brazil: Erythrostemon (1 sp.), Cenostigma (7 spp.), Libidibia (1 sp.), and Paubrasilia (1 sp.). The last three genera are placed in different clades in the Caesalpinia Group phylogeny, and yet they are characterized by having a numerically stable karyotype 2n = 24 (16 M+8A) and GC-rich heterochromatic bands (chromomycin A3 positive/CMA+ bands) in the proximal chromosome regions. To characterize the composition of their heterochromatin and test for the homology of these chromosomal regions, genomic DNA was extracted from Cenostigma microphyllum, Libidibia ferrea, and Paubrasilia echinata, and sequenced at low coverage using the Illumina platform. The genomic repetitive fractions were characterized using a Galaxy/RepeatExplorer-Elixir platform. The most abundant elements of each genome were chromosomally located by fluorescent in situ hybridization (FISH) and compared to the CMA+ heterochromatin distribution. The repetitive fraction of the genomes of C. microphyllum, L. ferrea, and P. echinata were estimated to be 41.70%, 38.44%, and 72.51%, respectively. Ty3/Gypsy retrotransposons (RT), specifically the Tekay lineage, were the most abundant repeats in each of the three genomes. FISH mapping revealed species-specific patterns for the Tekay elements in the proximal regions of the chromosomes, co-localized with CMA+ bands. Other species-specific patterns were observed, e.g., for the Ty3/Gypsy RT Athila elements which were found in all the proximal heterochromatin of L. ferrea or restricted to the acrocentric chromosomes of C. microphyllum. This Athila labeling co-localized with satellite DNAs (satDNAs). Although the Caesalpinia Group diverged around 55 Mya, our results suggest an ancestral colonization of Tekay RT in the proximal heterochromatin. Thus, the present-day composition of the pericentromeric heterochromatin in these Northeast Brazilian species is a combination of the maintenance of an ancestral Tekay distribution with a species-specific accumulation of other repeats.

中文翻译：

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进化趋同还是同源？Caesalpinia 组物种（豆科）的比较细胞基因组学揭示了着丝粒周围异染色质成分的多样化

主要结论我们通过细胞基因组学分析证明，巴西东北部 Caesalpinia 组的近端异染色质富含系统发育保守的 Ty3/Gypsy-Tekay RT，但在 Ty3/Gypsy-Athila RT 和 satDNA 的存在下存在差异。 摘要 Caesalpinia 组包括 225物种和 27 个单系属，其中 4 个出现在巴西东北部：Erythrostemon (1 sp.)、Cenostigma (7 spp.)、Libidibia (1 sp.) 和 Paubrasilia (1 sp.)。最后三个属位于 Caesalpinia Group 系统发育的不同进化枝中，但它们的特征是具有数值稳定的核型 2n = 24 (16 M+8A) 和富含 GC 的异染色带（色霉素 A3 阳性/CMA+ 带）近端染色体区域。为了表征它们的异染色质的组成并测试这些染色体区域的同源性，从小叶仙人掌、Libidibia ferrea 和 Paubrasilia echinata 中提取基因组 DNA，并使用 Illumina 平台以低覆盖率进行测序。使用 Galaxy/RepeatExplorer-Elixir 平台表征基因组重复部分。每个基因组中最丰富的元素通过荧光原位杂交 (FISH) 进行染色体定位，并与 CMA+ 异染色质分布进行比较。C. microphyllum、L. ferrea 和 P. echinata 基因组的重复部分估计分别为 41.70%、38.44% 和 72.51%。Ty3/Gypsy 逆转录转座子 (RT)，特别是 Tekay 谱系，是三个基因组中每一个中最丰富的重复序列。FISH 作图揭示了染色体近端区域 Tekay 元素的物种特异性模式，与 CMA+ 条带共定位。观察到其他物种特异性模式，例如，对于在 L. ferrea 的所有近端异染色质中发现的或仅限于 C. microphyllum 的近端着丝粒染色体的 Ty3/Gypsy RT Athila 元素。这种 Athila 标记与卫星 DNA (satDNA) 共定位。尽管 Caesalpinia 组在 55 Mya 左右分歧，但我们的结果表明 Tekay RT 在近端异染色质中的祖先定植。因此，这些巴西东北部物种中着丝粒周围异染色质的现今组成是维持祖先 Tekay 分布与其他重复序列的物种特异性积累的组合。