A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes

BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions harboring selected variants overlapped among the wheat genomes in any given wheat line. These selected regions are enriched for loci associated with agronomic traits detected in genome-wide association studies. CONCLUSIONS: Evidence suggests that directional selection in allopolyploids rarely acted on multiple parallel advantageous mutations across homoeologous regions, likely indicating that a fitness benefit could be obtained by a mutation at any one of the homoeologs. Additional advantageous variants in other homoelogs probably either contributed little benefit, or were unavailable in populations subjected to directional selection. We hypothesize that allopolyploidy may have increased the likelihood of beneficial allele recovery by broadening the set of possible selection targets

COMMON GOOSE BARNACLES LEPAS AUSTRALIS (THORACICA, PEDUNCULATA) ON DECEASED MAGELLANIC PENGUINS SPHENISCUS MAGELLANICUS (AVES)

Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo - FAPESP [2009/53956-9, 2010/51801-5]Conselho Nacional de Desenvolvimento Cientifico e Tecnologico - CNPq [301517/2006-1]Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq

Diagrammatic representation of the distribution of mutations identified by classical TILLING and by SCAMPRing.

<p>The BnSAD gene was used as a test to compare the effectiveness of NGS sequencing (SCAMPRing) vs. classical TILLING. Purple arrows indicate silent changes in the gene that are predicted to have no effect on the protein gene product. Black arrows indicate predicted missense mutations that alter the amino acid sequence of the protein product. Red arrows indicate predicted nonsense mutations that result in premature truncation of the protein. Circles indicate mutations that were detected using SCAMPRing but not originally found with classical TILLING.</p

Sequencing read depth and mutation frequencies identified in 384 lines of the <i>B. napus</i> population.

<p>The top panel represents the coverage of Illumina read depth (vertical axis) across the four amplicons developed for the target gene (bn1); a total of 1,530 bp (horizontal axis). The second, third and bottom panels represent the frequency (vertical axis) of candidate mutations (C to T, G to A, and A to G, respectively) identified in three pools (circled in red) of the 12 pools used in the analysis across the length of the target region in base pairs (horizontal axis). No A to G mutations were identified in the target locus and this is consistent with the mechanism of mutation induction by EMS.</p

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement

Host factors are associated with vaginal microbiome structure in pregnancy in the ECHO Cohort Consortium

Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we analyzed 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy both within and across diverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy, examined whether host factors were conserved across populations, and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, lower education, rather than self-identified race, remained a robust predictor of L. iners dominant (CST III) and diverse (CST IV) (OR = 8.44, 95% CI = 4.06–17.6 and OR = 4.18, 95% CI = 1.88–9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christensenii and Gardnerella spp.) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies