J. Pires

Publications205
h-index66
Citations18,335
Highly Influential Citations1,138
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The genome of the mesopolyploid crop species Brassica rapa
TLDR
The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
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Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome
TLDR
The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
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Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype[W][OA]
TLDR
Genetic, epigenetic, gene expression, and phenotypic changes in ∼50 resynthesized Brassica napus lines independently derived by hybridizing double haploids of Brassica oleracea and Brassica rapa indicate that exchanges among homoeologous chromosomes are a major mechanism creating novel allele combinations and phenotypesic variation in newly formed B. napus polyploids.
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The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
TLDR
A draft genome sequence of Brassica oleracea is described, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks.
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Understanding mechanisms of novel gene expression in polyploids.
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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels
TLDR
Putatively orthologous, shared single copy nuclear genes provide a vast source of new evidence for plant phylogenetics, genome mapping, and other applications, as well as a substantial class of genes for which functional characterization is needed.
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Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus
Polyploidy has contributed to the evolution of eukaryotes, particularly flowering plants. The genomic consequences of polyploidy have been extensively studied, but the mechanisms for chromosome…
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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.
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Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons
TLDR
It is shown that multiple origins of a polyploid species not only affect patterns of genetic variation in natural populations, but also contribute to differential patterns of gene expression and may therefore play a major role in the long-term evolution of polyploids.
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Current perspectives and the future of domestication studies
TLDR
It is argued that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.
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