15 research outputs found
Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
peer reviewedThe RADseq technology allows researchers to efficiently develop thousands of polymorphic
loci across multiple individuals with little or no prior information on the genome.
However, many questions remain about the biases inherent to this technology.
Notably, sequence misalignments arising from paralogy may affect the development of
single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity.
We evaluated the impact of putative paralog loci on genetic diversity estimation during
the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia
pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative
paralogous RAD loci as a function of both the depth of coverage and the mismatch
threshold allowed between loci. Putative paralogy was detected in a very variable
number of loci, from 1% to more than 20%, with the depth of coverage having a major
influence on the result. Putative paralogy artificially increased the observed degree of
polymorphism and resulting estimates of diversity. The choice of the depth of coverage
also affected diversity estimation and SNP validation: A low threshold decreased
the chances of detecting minor alleles while a high threshold increased allelic dropout.
SNP validation was better for the low threshold (4Ă—) than for the high threshold (18Ă—)
we tested. Using the strategy developed here, we were able to validate more than 80%
of the SNPs tested by means of individual genotyping, resulting in a readily usable set
of 330 SNPs, suitable for use in population genetics applications
Arabidopsis Fatty Acid Desaturase FAD2 Is Required for Salt Tolerance during Seed Germination and Early Seedling Growth
Fatty acid desaturases play important role in plant responses to abiotic stresses. However, their exact function in plant resistance to salt stress is unknown. In this work, we provide the evidence that FAD2, an endoplasmic reticulum localized ω-6 desaturase, is required for salt tolerance in Arabidopsis. Using vacuolar and plasma membrane vesicles prepared from the leaves of wild-type (Col-0) and the loss-of-function Arabidopsis mutant, fad2, which lacks the functional FAD2, we examined the fatty acid composition and Na+-dependent H+ movements of the isolated vesicles. We observed that, when compared to Col-0, the level of vacuolar and plasma membrane polyunsaturation was lower, and the Na+/H+ exchange activity was reduced in vacuolar and plasma membrane vesicles isolated from fad2 mutant. Consistent with the reduced Na+/H+ exchange activity, fad2 accumulated more Na+ in the cytoplasm of root cells, and was more sensitive to salt stress during seed germination and early seedling growth, as indicated by CoroNa-Green staining, net Na+ efflux and salt tolerance analyses. Our results suggest that FAD2 mediated high-level vacuolar and plasma membrane fatty acid desaturation is essential for the proper function of membrane attached Na+/H+ exchangers, and thereby to maintain a low cytosolic Na+ concentration for salt tolerance during seed germination and early seedling growth in Arabidopsis
Effect of NaCl on leaf H+-ATPase and the relevance to salt tolerance in two contrasting poplar species
Differential expression of four members of the H+ -ATPase gene family during dormancy of vegetative buds of peach trees
absen
Molecular characterization of a WEE1 gene homologue in tomato (Lycopersicon esculentum Mill.)
International audienc
FastqcReports
reports about the quality of sequencing of each of the nine sequenced individuals of Robinia pseudoacaci
The anaphase promoting complex activator CCS52A, a key factor for fruit growth and endoreduplication in tomato
Tomato fruit growth is characterized by the occurrence of numerous rounds of DNA endoreduplication in connection to cell expansion and final fruit size determination. Endoreduplication occurs as an impairment of mitosis, which can originate from the selective degradation of M-phase-specific cyclins via the ubiquitin-mediated proteolytic pathway, requiring the E3 ubiquitin ligase Anaphase Promoting Complex/Cyclosome (APC/C). In plants CCS52A is the ortholog of CDH1/FZR proteins from yeast, drosophila and human, belonging to the WD40-repeat protein family. During fruit development, the SlCCS52A gene expression is specifically associated to endoreduplication in tomato. Altering SlCCS52A expression in either negative or positive manner impacts the extent of endoreduplication in fruit and affects fruit size. When SlCCS52A is down-expressed endoreduplication is impaired during fruit growth leading to reduced fruit growth. However when SlCCS52A is overexpressed, endoreduplication is initially delayed, accounting for the altered final fruit size, but resumes and is even enhanced leading to fruit growth recovery, pointing at the physiological role of endoreduplication in growth induction during tomato fruit development