Genome evolution of wild barley ( Hordeum spontaneum ) by BARE -1 retrotransposon dynamics in response to sharp microclimatic divergence

Abstract

The replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The BARE-1 retrotransposon constitutes a major, dispersed, active component of Hordeum genomes, and BARE-1 number is positively correlated with genome size. We have examined genome size and BARE-1 insertion patterns and number in wild barley, Hordeum spontaneum, in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. BARE-1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the BARE-1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the BARE-1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the BARE-1 family to contribute to genome size growth. These local data are consistent with regional trends for BARE-1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.

DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel

“…Most previous studies of genetic diversity of wild barley in EC1 found a higher level of genetic diversity at SFS than NFS based on allozymes, DNA sequences of single genes (Yang et al, 2009) and copy number of BARE-1 retrotransposons (Kalendar et al, 2000). In contrast, REMAP (Retrotransposons-Microsatellite Amplified Polymorphism) analyses revealed more genotypes in the NFS than the SFS (Kalendar et al, 2000). Likewise, SSRs revealed a higher genetic diversity on the NFS than the SFS (Nevo et al, 2005).…”

“…The three clusters obtained with STRUCTURE differ in their level of genetic diversity, and the NFS accessions are about two times more diverse than the SFS accessions. Most previous studies of genetic diversity of wild barley in EC1 found a higher level of genetic diversity at SFS than NFS based on allozymes, DNA sequences of single genes (Yang et al, 2009) and copy number of BARE-1 retrotransposons (Kalendar et al, 2000). In contrast, REMAP (Retrotransposons-Microsatellite Amplified Polymorphism) analyses revealed more genotypes in the NFS than the SFS (Kalendar et al, 2000).…”

“…We investigated whether similar patterns of geographic population structure can be observed with DNA sequence data as with microsatellites or other marker types (Nevo et al, 1979(Nevo et al, , 2005Owuor et al, 1997;Kalendar et al, 2000;Hubner et al, 2012). Furthermore, we tested whether DNA sequencing of short genomic fragments confirms the high level of population differentiation of wild barley within the Nahal Oren Canyon that was observed in previous studies and inferred whether it is consistent with neutral demographic processes or local adaptation to the different slopes of the 'EC' .…”

Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

“…(12,13) have suggested that natural selection could be involved in regulating genome size, although a change in size is primarily due to the genome's tolerance for repeated sequences (5) and its ability to mobilize them (14). Intra-species variation in genome size has also been shown to be associated with environmental conditions in plants, and seems to involve mobilization of some transposable elements in plants (15), Drosophila (14,16), and pocket gophers (17). Any stressful conditions known to mobilize transposable elements, such as UV light, temperature, breeding conditions, etc.…”

The systematic value of nuclear DNA content for all species of Narcissus L. (Amaryllidaceae)

“…Repetitive DNA elements, including retro-transposons, are major components of eukaryotic genomes and such elements have a tendency towards amplification (Bennetzen and Kellogg 1997;Kalender et al 2000). Major decreases in genome size occur less frequently and such decreases have been observed especially following a doubling of the total genome by polyploidization (Ohri 1998), or the change from perennial to annual habit (Bennett 1972).…”