Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae

Abstract

Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33–2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2–12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.

Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA

“…These results together with our bioinformatics analysis of AcCen1K suggest that: (1) AcCen1K does not form long tandem arrays which is supported by the linear shape of RepeatExplorer cluster (Supplementary Figure 1), almost absence of discordantly mapped reads ( Figure 3B) and absence of FISH signals on A. cepa chromosomes and (2) based on the detection of the AfCen1K-FISH signals on four A. cepa chromosomes (Figure 2A) it can be speculated that true high-copy A. cepa centromeric has similarity to AfCen1K-specific region. Our results are in line with reports from other plant species demonstrating a high divergence of CTR sequences between closely related species or even between chromosomes of one species (Jiang et al, 2003;Gong et al, 2012;Melters et al, 2013;Comai et al, 2017;Su et al, 2019;Robledillo et al, 2020;Talbert and Henikoff, 2020). To the best of our knowledge the monomer size of AfCen1K is one of the largest among CENH3 associated CTR known to date.…”

“…The monomer size for most known CTRs shows a highly phased distribution with a peak around 150-180 bp corresponding to one wrap of the nucleosome (Melters et al, 2013;Yang et al, 2018). However, large CTRs monomers were previously characterized in Solanaceae (Gong et al, 2012), maize (Sharma et al, 2013), and Fabeae (Robledillo et al, 2018;Robledillo et al, 2020) species. Recent large-scale analysis of CENH3-associated CTRs in Fabeae indicated that 9 of 15 studied species have at least one CTR with monomer size >1,000 bp (Robledillo et al, 2020).…”

“…CRs can be associated with CENH3 histones as a unique member of the functional centromere as it was shown for Brassica nigra (Wang et al, 2019) or can be intermixed with CENH3-associated CTRs (Zhong et al, 2002;Kowar et al, 2016). CTRs were characterized in many plant species and their rapid divergence between species or even between chromosomes of a single set was demonstrated (Henikoff et al, 2001;Gong et al, 2012;Melters et al, 2013;Zhang et al, 2013;Robledillo et al, 2020). CTRs are organized into a long array of repeats with thousands of copies in the genome.…”

“…However, large-scale analysis of CTRs across different plant and animal species showed a broad diversity both in CTR monomer size and in GC content (Melters et al, 2013;Robledillo et al, 2020). The maximum monomer length of CTRs was found in Bos taurus taurus (1,419 bp; (Melters et al, 2013) for animals and in Fabeae (2,033-2,979 bp; Robledillo et al, 2018Robledillo et al, , 2020 and Solanacea (5,390 bp; Gong et al, 2012) for plants. Vicia faba is a species with a large monomer length, a large genome size (∼13 Gbp; Bennett and Smith, 1976) and large chromosomes.…”

“…The monomer size seems to be an important characteristic of CTRs for CENH3 nucleosome stability (Hasson et al, 2013;Zhang et al, 2013;Yang et al, 2018) and usually is between 100 and 200 bp (Melters et al, 2013). However, large-scale analysis of CTRs across different plant and animal species showed a broad diversity both in CTR monomer size and in GC content (Melters et al, 2013;Robledillo et al, 2020). The maximum monomer length of CTRs was found in Bos taurus taurus (1,419 bp; (Melters et al, 2013) for animals and in Fabeae (2,033-2,979 bp; Robledillo et al, 2018Robledillo et al, , 2020 and Solanacea (5,390 bp; Gong et al, 2012) for plants.…”