Chromosomal assignment of centromere-specific histone CENH3 genes in rye (Secale cereale L.) and their phylogeny

Abstract

Centromeres are essential for correct chromosome segregation during cell division and are determined by the presence of centromere-specific histone 3 (CENH3). Most of the diploid plant species, in which the structure and copy number of CENH3 genes have been determined, have this gene as a singleton; however, some cereal species in the tribe Triticeae have been found to have CENH3 in two variants. In this work, using the set of the wheat-rye addition lines we wanted to establish the chromosomal assignment of the CENH3 genes in the cultivated rye, Secale cereale (Linnaeus, 1753), in order to expand our knowledge about synteny conservation in the most important cereal species and about their chromosome evolution. To this end, we have also analyzed data in available genome sequencing databases. As a result, the αCENH3 and βCENH3 forms have been assigned to rye chromosomes 1R and 6R: specifically, the commonest variants αCENH3v1 and βCENH3v1 to chromosome 1R, and the rare variants, αCENH3v2 and probably βCENH3v2, to chromosome 6R. No other CENH3 variants have been found by analysis of the rye genome sequencing databases. Our chromosomal assignment of CENH3 in rye has been found to be the same as that in barley, suggesting that both main forms of CENH3 appeared in a Triticeae species before the barley and wheatrye lineages split.

Chromosome constitution and activity of the centromeric histone H3 (CENH3) variants in octoploid triticale lines

“…The distribution of rye-specific and wheat-specific SNPs in CENH3 sequencesfrom the triticale hybrids suggests a preferred synthesis of rye CENH3. This conclusion is in a good agreement with the fact that CENH3 genes are located on chromosome 1R (Lipikhina et al, 2017). A special case is the rye-specific substitution at position 73 of the αCENH3 nucleotide sequence, which is not present in the parental wheat cultivar.…”

Cytogenetic and molecular characteristics of rye genome in octoploid triticale (× Triticosecale Wittmack)

“…1b–f) in all hybrid plants, regardless of the chromosome number. Earlier, we have shown that genes encoding the main variants of the rye centromere histone H3 are localized on chromosome 1R (Lipikhina et al 2017). The rye-specific substitution at the position 73 of the α CENH3 coding sequence does not occur in the parent wheat variety Triple Dirk D. In triticale plants with different chromosome numbers (56, 49, 43) in generations F 3 -F 5 , the number of α CENH3 copies carrying this substitution increases from 16 to 57%.…”

Young retrotransposons and non‐B DNA structures promote the establishment of dominant rye centromere in the 1RS.1BL fused centromere

“…To further determine the size and location of fused centromere, we performed ChIP‐Seq using wheat αCENH3 antibody in two 1RS.1BL translocation cultivars AK58 and KN199, two rye lines Imperial (IMP) and Lo7. The employed antibody has the capability to recognize rye centromeres (Yuan et al ., 2015; Lipikhina et al ., 2017). We observed clear signals with distinct strengths in all centromeres of these lines using immunoprecipitated DNA as probe (Fig.…”

“…Chromatin immunoprecipitation sequencing (ChIP‐Seq) assay was carried out following the protocol described by Nagaki et al . (2003), using antibody that are specific to wheat CENH3 and capable of effectively identifying rye centromeres as well, the αCENH3 antibody peptide (RTKHPAVRKTK) utilized in our study was consistent for both wheat and rye (Yuan et al ., 2015; Lipikhina et al ., 2017). Additionally, antibodies for H3 trimethyl‐Lys 4 (Millipore) and H3 dimethyl‐Lys 9 (Millipore) were also employed in our analysis.…”