Contrasting evolutionary genome dynamics between domesticated and wild yeasts.
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ABSTRACT:
SUBMITTER: Yue JX
PROVIDER: S-EPMC5446901 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of Kluyveromyces lactis, a yeast species well known for its involvement in dairy processes and also present in natural environments. Using a combination of short- and long-read sequencing strategies, we investigated the genomic variability of 41 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10-2) compared with other species such as Saccharomyces cerevisiae (θw = 1.6 × 10-2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10-3), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation, and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.
| S-EPMC9897184 | biostudies-literature
Project description:The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.
| S-EPMC7295394 | biostudies-literature
Project description:BackgroundThe distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M. gallopavo populations including domesticated individuals.ResultsAnalyses of 612 wild and domesticated turkey mitochondrial D-loop sequences, including 187 that were collected for this study and 425 from databases, revealed 64 haplotypes with few mutations, some of which are shared between domesticated and wild turkeys. We found a high level of haplotype and nucleotide diversity, which suggests that the total population of this species is large and stable with an old evolutionary history. The results of genetic differentiation, haplotype network, and genealogical relationships analyses revealed three main genetic groups within the species: mexicana as a population relict (C1), merriami (C2), and mexicana/intermedia/silvestris/osceola (C3). Haplotypes detected in domesticated turkeys belong to group C3. Estimates of divergence times agree with range expansion and diversification events of the relict population of M. gallopavo in northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Demographic reconstruction showed that an expansion of the population occurred 110,000 to 130,000 years ago (Kya), followed by a stable period 100 Kya and finally a decline ~ 10 Kya (Pleistocene-Holocene boundary). In Mexico, the Trans-Mexican Volcanic Belt may be responsible for the range expansion of the C3 group. Two haplotypes with different divergence times, MGMDgoB/MICH1 and MICH2, are dominant in domesticated and commercial turkeys.ConclusionsDuring the Pleistocene, a large and stable population of M. gallopavo covered a wide geographic distribution from the north to the center of America (USA and Mexico). The mexicana, merriami, and mexicana/intermedia/silvestris/osceola genetic groups originated after divergence and range expansion from northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Old and new maternal lines of the mexicana/intermedia/silvestris/osceola genetic group were distributed within the Trans-Mexican Volcanic Belt where individuals were captured for domestication. Two haplotypes are the main founder maternal lines of domesticated turkeys.
| S-EPMC5905111 | biostudies-literature
Project description:Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.
| S-EPMC8476135 | biostudies-literature
Project description:BackgroundVariations in gene expression, mediated by epigenetic mechanisms, may cause broad phenotypic effects in animals. However, it has been debated to what extent expression variation and epigenetic modifications, such as patterns of DNA methylation, are transferred across generations, and therefore it is uncertain what role epigenetic variation may play in adaptation.ResultsIn Red Junglefowl, ancestor of domestic chickens, gene expression and methylation profiles in thalamus/hypothalamus differed substantially from that of a domesticated egg laying breed. Expression as well as methylation differences were largely maintained in the offspring, demonstrating reliable inheritance of epigenetic variation. Some of the inherited methylation differences were tissue-specific, and the differential methylation at specific loci were little changed after eight generations of intercrossing between Red Junglefowl and domesticated laying hens. There was an over-representation of differentially expressed and methylated genes in selective sweep regions associated with chicken domestication.ConclusionsOur results show that epigenetic variation is inherited in chickens, and we suggest that selection of favourable epigenomes, either by selection of genotypes affecting epigenetic states, or by selection of methylation states which are inherited independently of sequence differences, may have been an important aspect of chicken domestication.
| S-EPMC3297523 | biostudies-literature
Project description:The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. In this study we trace the evolutionary history of the NAM-B1 in tetraploid wheat species and evaluate it as a putative domestication gene.Genotyping of wild and landrace tetraploid accessions showed presence of only null alleles in durum. Domesticated emmer wheats contained both null alleles and the wild-type allele while wild emmers, with one exception, only carried the wild-type allele. One of the null alleles consists of a deletion that covers several 100 kb. The other null-allele, a one-basepair frame-shift insertion, likely arose among wild emmer. This allele was the target of a selective sweep, extending over several 100 kb.The NAM-B1 gene fulfils some criteria for being a domestication gene by encoding a trait of domestication relevance (seed size) and is here shown to have been under positive selection. The presence of both wild-type and null alleles in domesticated emmer does, however, suggest the gene to be a diversification gene in this species. Further studies of genotype-environment interactions are needed to find out under what conditions selection on different NAM-B1 alleles have been beneficial.
| S-EPMC5738170 | biostudies-literature
Project description:BackgroundThe species Zea mays includes both domesticated maize (ssp. mays) and its closest wild relatives known as the teosintes. While genetic and archaeological studies have provided a well-established history of Z. mays evolution, there is currently minimal description of its current and past distribution. Here, we implemented species distribution modeling using paleoclimatic models of the last interglacial (LI; ?135,000 BP) and the last glacial maximum (LGM; ?21,000 BP) to hindcast the distribution of Zea mays subspecies over time and to revisit current knowledge of its phylogeography and evolutionary history.Methodology/principal findingsUsing a large occurrence data set and the distribution modeling MaxEnt algorithm, we obtained robust present and past species distributions of the two widely distributed teosinte subspecies (ssps. parviglumis and mexicana) revealing almost perfect complementarity, stable through time, of their occupied distributions. We also investigated the present distributions of primitive maize landraces, which overlapped but were broader than those of the teosintes. Our data reinforced the idea that little historical gene flow has occurred between teosinte subspecies, but maize has served as a genetic bridge between them. We observed an expansion of teosinte habitat from the LI, consistent with population genetic data. Finally, we identified locations potentially serving as refugia for the teosintes throughout epochs of climate change and sites that should be targeted in future collections.Conclusion/significanceThe restricted and highly contrasting ecological niches of the wild teosintes differ substantially from domesticated maize. Variables determining the distributions of these taxa can inform future considerations of local adaptation and the impacts of climate change. Our assessment of the changing distributions of Zea mays taxa over time offers a unique glimpse into the history of maize, highlighting a strategy for the study of domestication that may prove useful for other species.
| S-EPMC3498274 | biostudies-literature
Project description:Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.
| S-EPMC4564799 | biostudies-literature
Project description:Bombyx mori and Bombyx mandarina are morphologically and physiologically similar. In this study, we compared the nucleotide variations in the complete mitochondrial (mt) genomes between the domesticated silkmoth, B. mori, and its wild ancestors, Chinese B. mandarina (ChBm) and Japanese B. mandarina (JaBm). The sequence divergence and transition mutation ratio between B. mori and ChBm are significantly smaller than those observed between B. mori and JaBm. The preference of transition by DNA strands between B. mori and ChBm is consistent with that between B. mori and JaBm, however, the regional variation in nucleotide substitution rate shows a different feature. These results suggest that the ChBm mt genome is not undergoing the same evolutionary process as JaBm, providing evidence for selection on mtDNA. Moreover, investigation of the nucleotide sequence divergence in the A+T-rich region of Bombyx mt genomes also provides evidence for the assumption that the A+T-rich region might not be the fastest evolving region of the mtDNA of insects.
| S-EPMC3036069 | biostudies-literature
Project description:The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
| S-EPMC9284676 | biostudies-literature