Kirov Ilya, Odintsov Sergey, Omarov Murad, Gvaramiya Sofya, Merkulov Pavel, Dudnikov Maxim, Ermolaev Alexey, Van Laere Katrijn, Soloviev Alexander, Khrustaleva Ludmila
Laboratory of Marker-assisted and genomic selection of plants, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.
Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.
Front Plant Sci. 2020 Oct 23;11:562001. doi: 10.3389/fpls.2020.562001. eCollection 2020.
The centromere is a unique part of the chromosome combining a conserved function with an extreme variability in its DNA sequence. Most of our knowledge about the functional centromere organization is obtained from species with small and medium genome/chromosome sizes while the progress in plants with big genomes and large chromosomes is lagging behind. Here, we studied the genomic organization of the functional centromere in and , both species with a large genome (13 Gb and 16 Gb/1C, 2 = 2 = 16) and large-sized chromosomes. Using low-depth DNA sequencing for these two species and previously obtained CENH3 immunoprecipitation data we identified two long (1.2 Kb) and high-copy repeats, AfCen1K and AcCen1K. FISH experiments showed that AfCen1K is located in all centromeres of chromosomes while no AcCen1K FISH signals were identified on chromosomes. Our molecular cytogenetic and bioinformatics survey demonstrated that these repeats are partially similar but differ in chromosomal location, sequence structure and genomic organization. In addition, we could conclude that the repeats are transcribed and their RNAs are not polyadenylated. We also observed that these repeats are associated with insertions of retrotransposons and plastidic DNA and the landscape of and centromeric regions possess insertions of plastidic DNA. Finally, we carried out detailed comparative satellitome analysis of and genomes and identified a new chromosome- and -specific tandem repeat, TR2CL137, located in the centromeric region. Our results shed light on the centromere organization and provide unique data for future application in genome annotation.
着丝粒是染色体的一个独特部分，它将保守功能与DNA序列的极端变异性结合在一起。我们对功能性着丝粒组织的大部分了解来自基因组/染色体大小为中小的物种，而在基因组大且染色体大的植物方面进展滞后。在这里，我们研究了基因组大（13 Gb和16 Gb/1C，2n = 2x = 16）且染色体大的物种和的功能性着丝粒的基因组组织。利用这两个物种的低深度DNA测序以及先前获得的CENH3免疫沉淀数据，我们鉴定出两个长（1.2 Kb）且高拷贝的重复序列，AfCen1K和AcCen1K。荧光原位杂交（FISH）实验表明，AfCen1K位于染色体的所有着丝粒中，而在染色体上未鉴定到AcCen1K的FISH信号。我们的分子细胞遗传学和生物信息学调查表明，这些重复序列部分相似，但在染色体位置、序列结构和基因组组织上存在差异。此外，我们可以得出结论，这些重复序列被转录，且其RNA没有多聚腺苷酸化。我们还观察到这些重复序列与反转录转座子和质体DNA的插入有关，并且和着丝粒区域的景观具有质体DNA的插入。最后，我们对和基因组进行了详细的比较卫星基因组分析，并鉴定出一个位于着丝粒区域的新的染色体和特异性串联重复序列TR2CL137。我们的结果揭示了着丝粒组织，并为未来在基因组注释中的应用提供了独特的数据。
