Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.
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SUBMITTER: Hu H
PROVIDER: S-EPMC9292397 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
Publications
Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.
Hu Haifei H Scheben Armin A Verpaalen Brent B Tirnaz Soodeh S Bayer Philipp E PE Hodel Richard G J RGJ Batley Jacqueline J Soltis Douglas E DE Soltis Pamela S PS Edwards David D
The New phytologist 20210819 4
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Project description:BackgroundStructural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation.ResultsIn this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement.ConclusionsThese findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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Project description:Background and aimsAt the population level, genetic diversity is a key determinant of a tree species' capacity to cope with stress. However, little is known about the relative importance of the different components of genetic diversity for tree stress responses. We compared how two sources of genetic diversity, genotype and cytotype (i.e. differences in ploidy levels), influence growth, phytochemical and physiological traits of Populus tremuloides in the presence and absence of environmental stress.MethodsIn a series of field studies, we first assessed variation in traits across diploid and triploid aspen genotypes from Utah and Wisconsin under non-stressed conditions. In two follow-up experiments, we exposed diploid and triploid aspen genotypes from Wisconsin to individual and interactive drought stress and defoliation treatments and quantified trait variations under stress.Key resultsWe found that (1) tree growth and associated traits did not differ significantly between ploidy levels under non-stressed conditions. Instead, variation in tree growth and most other traits was driven by genotypic and population differences. (2) Genotypic differences were critical for explaining variation of most functional traits and their responses to stress. (3) Ploidy level played a subtle role in shaping traits and trait stress responses, as its influence was typically obscured by genotypic differences. (4) As an exception to the third conclusion, we showed that triploid trees expressed 17 % higher foliar defence (tremulacin) levels, 11 % higher photosynthesis levels and 23 % higher rubisco activity under well-watered conditions. Moreover, triploid trees displayed greater drought resilience than diploids as they produced 35 % more new tissue than diploids when recovering from drought stress.ConclusionAlthough ploidy level can strongly influence the ecology of tree species, those effects may be relatively small in contrast to the effects of genotypic variation in highly diverse species.
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Project description:Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology. The distribution of PAV was studied in a mussel chromosome-level genome assembly, revealing a widespread distribution but with hotspots of dispensability. Special attention was given to the effect of PAV in gene expression, since dispensable genes were found to be inherently subject to distortions due to their sparse distribution among individuals. Furthermore, the high expression and strong tissue specificity of some dispensable genes, such as myticins, strongly supported their biological relevance. The significant differences in the repertoire of dispensable genes associated with two geographically distinct populations suggest that PAV is involved in local adaptation. Overall, the PAV phenomenon would provide a key selective advantage at the population level.
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Project description:BackgroundGene presence/absence (P/A) polymorphisms are commonly observed in plants and are important in individual adaptation and species differentiation. Detecting their abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms in a given species. The recently sequenced 80 Arabidopsis genomes provide an opportunity to address these questions.ResultsBy systematically investigating these accessions, we identified 2,407 P/A genes (or 8.9%) absent in one or more genomes, averaging 444 absent genes per accession. 50.6% of P/A genes belonged to multi-copy gene families, or 31.0% to clustered genes. However, the highest proportion of P/A genes, outnumbered in singleton genes, was observed in the regions near centromeres. In addition, a significant correlation was observed between the P/A gene frequency among the 80 accessions and the diversity level at P/A loci. Furthermore, the proportion of P/A genes was different among functional gene categories. Finally, a P/A gene tree showed a diversified population structure in the worldwide Arabidopsis accessions.ConclusionsAn estimate of P/A genes and their frequency distribution in the worldwide Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes, by which individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.
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Project description:rs08-01_met2 - comparative analysis of catma chips with a met2 overexpression line - Role of the MET2 methyltransferase on methylation and gene expression in arabidopsis - Comparison of transcription in roots and aerial parts of one week-old plants from two lines (WT and MET2 overexpressor) Keywords: organ comparison,wt vs mutant comparison
2009-05-28 | GSE11563 | GEO
Project description:rs08-01_met2 - comparative analysis of catma chips with a met2 overexpression line - Role of the MET2 methyltransferase on methylation and gene expression in arabidopsis - Comparison of transcription in roots and aerial parts of one week-old plants from two lines (WT and MET2 overexpressor) Keywords: organ comparison,wt vs mutant comparison 4 dye-swap - CATMA arrays
2010-05-18 | E-GEOD-11563 | biostudies-arrayexpress
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