Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae

Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences

Whole-Genome Sequencing and Intraspecific Analysis of the Yeast Species Lachancea quebecensis

The gold standard in yeast population genomics has been the model organism Saccharomyces cerevisiae. However, the exploration of yeast species outside the Saccharomyces genus is essential to broaden the understanding of genome evolution. Here, we report the analyses of whole-genome sequences of nineisolates from the recently described yeast species Lachancea quebecensis. The genome of one isolate was assembled and annotated, and the intraspecific variability within L. quebecensis was surveyed by comparing the sequences from the eight other isolates to this reference sequence. Our study revealed that these strains harbor genomes with an average nucleotide diversity of pi = 2 x 10(-3) which is slightly lower, although on the same order of magnitude, as that previously determined for S. cerevisiae (pi = 4 x 10(-3)). Our results show that even though these isolates were all obtained from a relatively isolated geographic location, the same ecological source, and represent a smaller sample size than is available for S. cerevisiae, the levels of divergence are similar to those observed in this model species. This divergence is essentially linked to the presence of two distinct clusters delineated according to geographic location. However, even with relatively similar ranges of genome divergence, L. quebecensis has an extremely low global phenotypic variance of 0.062 compared with 0.59 previously determined in S. cerevisiae

Genetic analysis of artificial Triticinae amphidiploid Aurotica based on the glaucousness trait

Changes in plant genomes of hybrid origin which become apparent on different levels of phenotypic manifestation of genetic and epigenetic changes are an important object of cytogenetics and molecular genetics. The changes in expression of the glaucousness trait in the artificial Triticinae amphidiploid Aurotica (AABBTT) were investigated; haplotypes of plants with the appearance of glaucous and non-glaucous genes were determined by hybridization experiments. It was suppoted that the changes in expression can be explained by (epi)mutations abolishing the efficiency of dominant alleles of orthologous series of glaucous inhibitor gene Iw. Analysis of F2 population with SSR markers specific to 2B and 2D wheat chromosomes and 2T chromosome of Aegilops mutica manifested associated inheritance of the Wms 102 and Wms 702 loci, which mapped to the short arm of chromosome 2D. The Wms 702 marker was linked to the Iw2(T) gene and can now be used to detect that gene.Изменения в геноме растений гибридного проис-хождения, которые проявляются на разных фенотипических уровнях реализации генетических и эпигенетических изменений, интенсивно исследуются цитогенетикой и молекулярной генетикой. Изучали изменения экспрессии признака наличие/отсутствие воскового налета у искусственного амфидиплоида Авротика (Triticinae, AABBTT). Гибридологическим анализом установлены гаплотипы растений с контрастными фенотипами и показано, что изменение экспрессии признака связано с (эпи)мутацией, которая приводит к утрате активности доминантного аллеля ортологической серии генов Iw —ингибиторов воскового налета у пшеницевых. Микросателлитный анализ расщепляющихся популяций по SSR-локусам, специфичным для 2B и 2D хромосом пшеницы и 2T хромосомы эгилопса, показал сцепленное наследование локусов Wms 102 и Wms 702, локализованных на плече 2DS, а локус Wms 702 сцеплен с геном Iw2(T) и может быть использован для определения этого гена.Зміни у геномі рослин гібридного походження, які виявляються на різних фенотипних рівнях реалізації генетичних та епігенетичних змін, інтенсивно досліджуються цитогенетикою та молекулярною генетикою. Вивчали зміни експресії ознаки наявність/відсутність воскової осуги у штучного амфідиплоїда Авротика (Triticinae, AABBTT). Гібридологічним аналізом встановлено гаплотипи рослин з контрастними фенотипами та показано, що зміна експресії ознаки пов’язана з (епі)мутацією, яка призводить до втрати активності домінантного алеля ортологічної серії генів Iw — інгібіторів воскової осуги у пшеницевих. Мікросателітний аналіз популяций, що розщеплюються, за SSR-локусами, специфічними для 2B та 2D хромосом пшениці та 2T хромосоми егілопсу, показав зчеплене успадкування локусів Wms 102 та Wms 702, локалізованих на плечі 2DS, а локус Wms 702 зчеплений з геном Iw2(T) та може бути використаний для визначення цього гена

Ecological networks to unravel the routes to horizontal transposon transfers

Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs