Screening diversity and distribution of Copia retrotransposons reveals a specific amplification of BARE1 elements in genomes of the polyploid Hordeum murinum complex

Abstract

We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.

How diverse a monocentric chromosome can be? Repeatome and centromeric organization of Juncus effusus (Juncaceae)

“…It differs from the uniformly dispersed pattern in the large chromosomes of L. elegans (Heckmann et al., 2013). Outside cyperids, in the large monocentric genome of Hordeum murinum (1C = ~8 Gbp), a set of Ty1/copia probes, including different lineages from the Angela clade, also showed a uniform distribution on chromosomes, except in the centromeric region and nucleolus‐organizing regions (Ourari et al., 2020), indicating that genome size also has a major influence on genome organization.…”

Genetic diversity, population structuring and expansion history of Coronilla scorpioides

“…The percentage of the polymorphic band identified in C. scorpioides by REMAP markers was higher than that obtained in Medicago sativa (Mandoulakani et al, 2012) and Triticum aestivum (Holasou et al, 2019). In this sense, the insertion polymorphism resulting from the element's integration could differentiate lines, groups of lines, or even species (Ourari et al, 2020). In higher eukaryotes, essentially plants and vertebrates, there is, generally, little convergence of insertion, i.e., an insertion found at the same location in two genotypes will reflect an insertion present in an ancestor common to both genotypes.…”