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Retrotransposon-based molecular markers were applied for the first time within the genera Xanthosoma and Colocasia to assess intraspecific variability among 27 accessions of cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esulenta). Over 16 distinct retrotransposon fragments were isolated, sequenced, and LTR primers were designed to obtain Inter-Retrotransposon Amplified Polymorphism (IRAP) fingerprints. The set of six polymorphic LTR primers yielded 433 reproducible bands across a set of 20 X. sagittifolium samples. Out of the 433 bands, 400 fragments (92%) were polymorphic. In seven C. esculenta accessions, the six primers amplified a total of 354 reproducible, informative data points, of which 285 (80.5%) were polymorphic. Data concerning the number of polymorphic bands and Shannon’s index in X. sagittifolium accessions suggest that retrotransposon activity continued after Xanthosoma speciation. Cluster analysis placed all the accessions in two groups according to their species delimitation. The accessions of X. sagittifolium were further divided into two subgroups corresponding to their ploidy level. Moreover, our results showed that the genetic variability accessed by IRAP markers allows separation of X. sagittifolium and C. esculenta accessions according to their type and botanical variety respectively. These data provide a basis for better germplasm management, future systematic studies and genetic improvement, as well as for exploration of the role of retrotransposons in cocoyam and taro polyploid formation and genome dynamics.

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A., published version, peerReviewed

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Genomic structural differences among individuals, particularly copy number variation (CNV), are of great importance in the exploration of mammalian diversity and evolution. CNV is implicated in diverse human diseases including nervous system, neurological, and autoimmune disorders. Here, we aimed to detect and evaluate CNV for four genes: grin1 that is multifunctional in the regulation of normal and pathological brain functions; three housekeeping genes with stable expression, gapdh, rpl13a, and ywhaz. These were examined in rat strains differing in excitability of the nervous systems. The rpl13a copy number is significantly reduced in both the hippocampus and bone marrow in rats with a high excitability threshold (HT). In bone marrow of rats with a low excitability threshold (LT), there is a two fold increase in the rpl13a copy numbervs Wistar rats. Stress is also connected to a decrease rpl13a copy number in the bone marrow of HT ( emotional hypokinetic stress) and Wistar rats (emotional painful stress). The observed phenomenon may be associated with the role of rpl13 a in lipid metabolism; synaptic membranes of the HT cerebral cortex had significantly higher amounts of sphingomyelin and phosphatidylcholine.

The replication of Long Terminal Repeat (LTR) retrotransposons, which can constitute over 80% of higher plant genomes, resembles that of retroviruses. A major question for retrotransposons and retroviruses is how the two conflicting roles of their transcripts, in translation and reverse transcription, are balanced. Here, we show that the BARE retrotransposon, despite its organization into just one open reading frame, produces three distinct classes of transcripts. One is capped, polyadenylated, and translated, but cannot be copied into cDNA. The second is not capped or polyadenylated, but is destined for packaging and ultimate reverse transcription. The third class is capped, polyadenylated, and spliced to favor production of a subgenomic RNA encoding only Gag, the protein forming virus-like particles. Moreover, the BARE2 subfamily, which cannot synthesize Gag and is parasitic on BARE1, does not produce the spliced sub-genomic RNA for translation but does make the replication competent transcripts, which are packaged into BARE1 particles. To our knowledge, this is first demonstration of distinct RNA pools for translation and transcription for any retrotransposon.

Timothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers. Using four primer combinations, 533 REMAP markers were analyzed, compared with 464 polymorphic alleles in the 13 SSR loci previously. The average marker index, which describes information obtained per experiment (per primer combination or locus) was over six times higher with REMAPs. Most of the variation found was within accessions, with somewhat less, 89 %, for REMAPs, than for SSR, with 93 %. SSRs revealed differences in the level of diversity slightly better than REMAPs but neither marker type could reveal any clear clustering of accessions based on countries, vegetation zones, or different cultivar types. In our study, reliable evaluation of SSR allele dosages was not possible, so each allele had to be handled as a dominant marker. SSR and REMAP, which report from different mechanisms of generating genetic diversity and from different genomic regions, together indicate a lack of population structure. Taken together, this likely reflects the outcrossing and hexaploid nature of timothy rather than failures of either marker system.