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

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.

Diversity and evolution of the Hordeum murinum polyploid complex in Algeria.

Population diversity and evolutionary relationships in the Hordeum murinum L. polyploid complex were explored in contrasted bioclimatic conditions from Algeria. A multidisciplinary approach based on morphological, cytogenetic, and molecular data was conducted on a large population sampling. Distribution of diploids (subsp. glaucum) and tetraploids (subsp. leporinum) revealed a strong correlation with a North-South aridity gradient. Most cytotypes exhibit regular meiosis with variable irregularities in some tetraploid populations. Morphological analyses indicate no differentiation among taxa but high variability correlated with bioclimatic parameters. Two and three different nuclear sequences (gene coding for an unspliced genomic protein kinase domain) were isolated in tetraploid and hexaploid cytotypes, respectively, among which one was identical with that found in the diploid subsp. glaucum. The tetraploids (subsp. leporinum and subsp. murinum) do not exhibit additivity for 5S and 45S rDNA loci comparative with the number observed in the related diploid (subsp. glaucum). The subgenomes in the tetraploid taxa could not be differentiated using genomic in situ hybridization (GISH). Results support an allotetraploid origin for subsp. leporinum and subsp. murinum that derives from the diploid subsp. glaucum and another unidentified diploid parent. The hexaploid (subsp. leporinum) has an allohexaploid origin involving the two genomes present in the allotetraploids and another unidentified third diploid progenitor.