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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
TLDR
It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. Expand
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
TLDR
Sequencing of genomes from three Brassicaceae species and their joint analysis with six previously sequenced crucifer genomes confirm that most of the identified CNSs are evolving under medium to strong purifying selection, and highlight both similarities and several key differences between the regulatory DNA of plants and other species. Expand
Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences.
TLDR
The results show unequivocally that, in contrast to the endonuclease-resistant sperm chromatin packaged by protamines, regions of increased end onuclease sensitivity are closely associated with gene regulatory regions, including many promoter sequences and sequences recognized by CCCTC-binding factor (CTCF). Expand
Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs.
TLDR
A cross-platform microarray strategy was used to assess the profile of human spermatozoal transcripts from fertile males who had fathered at least one child compared to teratozoospermic individuals and revealed the transcriptional perturbation common to the affected individuals. Expand
The butterfly plant arms-race escalated by gene and genome duplications
TLDR
The coevolutionary interactions between plants and butterflies are examined, and evidence for an escalating evolutionary arms-race is uncovered, providing an important connection between the origins of biodiversity, coev evolution, and the role of gene and genome duplications as a substrate for novel traits. Expand
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
TLDR
The transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection, similar to that seen in Arabidopsis, which self fertilization evolved about 1 million years ago. Expand
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora
TLDR
Overall, the results suggest that both positive and negative selection on plant noncoding sequence are considerably rarer than in animal genomes. Expand
Identification of human sperm transcripts as candidate markers of male fertility
TLDR
Through the analyses of the spermatozoal transcriptome from 24 donors of proven fertility, a series of transcripts that were consistently present among all individuals were identified, suggesting that among the heterogeneity observed in the sperm transcriptome, a distinct set is strictly regulated. Expand
The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice
TLDR
The results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. Expand
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
TLDR
The results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a “head start” through a legacy of deleterious variants and differential expression originating in parental diploids populations. Expand
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