Allopolyploidy and the complex phylogenetic relationships within the Hordeum brachyantherum taxon

Phylogenetic analysis of two single-copy nuclear genes revealed origin of tetraploid barley Hordeum marinum

Sea barley Hordeum marinum is an important germplasm resource. However, the origin of this tetraploid H. marinum subsp. gussoneanum is still unclear, which has caused great perplexity to the exploration and utilization of germplasm resources. We used two single-copy nuclear genes, thioredoxin-like gene (TRX) and waxy1 gene encoding granule-bound starch synthase (WAXY1) to analyze 41 accessions of Hordeum marinum. The phylogenies of different genes told different story of evolution of tetraploids of H. marinum subsp. gussoneanum. The phylogenetic trees showed that two distinct copies of sequences from both genes were detected for some accessions of the tetraploids of H. marinum subsp. gussoneanum, and diploid marinum might also contribute to the origin and evolution of the tetraploid gussoneanum. Our findings suggested that tetraploid more likely originated from the diploids of H. marinum subsp. gussoneanum and another ancestor that might be an extinct unknown diploid species. Homogenization of gene in tetraploids also occurred after polyploidization as both TRX and WAXY1 sequences in some accessions of tetraploid H. marinum subsp. gussoneanum cannot be distinguished, indicating the complicated evolution of this tetraploid.

Comparative karyotype analysis among six species of Ipomoea based on two newly identified repetitive sequences

Sweet potato is one of the most important crops worldwide; however, basic research in this crop is limited. In this study, we aimed to construct a detailed karyotype of six species of Ipomoea (hexaploid Ipomoea batatas and five related species, namely, one tetraploid, I. tabascana and four diploids, I. splendor-sylvae, I. trifida, I. tenuissima, and I. × leucantha) and understand the relationship among these species. Two satellite repeats (viz., Itf_1 and Itf_2) were identified from the diploid I. trifida genome sequence using RepeatExplorer on Galaxy. Together with the ribosomal DNA (rDNA), although without distinguishable chromosomes, a detailed karyotype was constructed for the six species. Our results showed a similar karyotype between I. tenuissima and I. × leucantha, indicating their close relationship. The signal distribution pattern of Itf_1, 45S rDNA combination, detected only in I. trifida, I. tabascana, and I. batatas, implied their close relationships. The chromosomes carrying 5S rDNA could be conserved among the six species as they always carried the Itf_2 signals, which generated a similar signal distribution pattern. The results enabled a detailed comparative cytogenetic analysis, providing valuable information to understand the relationship among these species and help assemble the genome sequence of the six species of Ipomoea.

On the allopolyploid origin and genome structure of the closely related species Hordeum secalinum and Hordeum capense inferred by molecular karyotyping

BACKGROUND AND AIMS

To provide additional information to the many phylogenetic analyses conducted within Hordeum , here the origin and interspecific affinities of the allotetraploids Hordeum secalinum and Hordeum capense were analysed by molecular karyotyping.

METHODS

Karyotypes were determined using genomic in situ hybridization (GISH) to distinguish the sub-genomes and , plus fluorescence in situ hybridization (FISH)/non-denaturing (ND)-FISH to determine the distribution of ten tandem repetitive DNA sequences and thus provide chromosome markers.

KEY RESULTS

Each chromosome pair in the six accessions analysed was identified, allowing the establishment of homologous and putative homeologous relationships. The low-level polymorphism observed among the H. secalinum accessions contrasted with the divergence recorded for the sub-genome of the H. capense accessions. Although accession H335 carries an intergenomic translocation, its chromosome structure was indistinguishable from that of H. secalinum .

CONCLUSION

Hordeum secalinum and H. capense accession H335 share a hybrid origin involving Hordeum marinum subsp. gussoneanum as the genome donor and an unidentified genome progenitor. Hordeum capense accession BCC2062 either diverged, with remodelling of the sub-genome, or its genome was donated by a now extinct ancestor. A scheme of probable evolution shows the intricate pattern of relationships among the Hordeum species carrying the genome (including all H. marinum taxa and the hexaploid Hordeum brachyantherum ).

Sequencing of long stretches of repetitive DNA

Repetitive DNA is widespread in eukaryotic genomes, in some cases making up more than 80% of the total. SSRs are a type of repetitive DNA formed by short motifs repeated in tandem arrays. In some species, SSRs may be organized into long stretches, usually associated with the constitutive heterochromatin. Variation in repeats can alter the expression of genes, and changes in the number of repeats have been linked to certain human diseases. Unfortunately, the molecular characterization of these repeats has been hampered by technical limitations related to cloning and sequencing. Indeed, most sequenced genomes contain gaps owing to repetitive DNA-related assembly difficulties. This paper reports an alternative method for sequencing of long stretches of repetitive DNA based on the combined use of 1) a linear vector to stabilize the cloning process, and 2) the use of exonuclease III for obtaining progressive deletions of SSR-rich fragments. This strategy allowed the sequencing of a fragment containing a stretch of 6.2 kb of continuous SSRs. To demonstrate that this procedure can sequence other kinds of repetitive DNA, it was used to examine a 4.5 kb fragment containing a cluster of 15 repeats of the 5S rRNA gene of barley.