Recent Posts

Review: Orphan crops and their wild relatives in the genomic era (Mol. Plant)

More than half of human calories come from rice, wheat, and corn, although many other cereals have been domesticated as food crops. Several of these “orphan” cereal crops and their wild relatives are being studied with the goal of diversifying our food supply, which is particularly important due…

ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks (Plant Physiology)

ConnecTF: A platform to integrate transcription factor-gene interactions and validate regulatory networks Gene regulatory networks (GFNs) are complex beasts, integrating multiple components of transcription factors (TFs), regulatory loci, and function -- not to mention the myriad datasets and methodologies…

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research (Nucleic Acids Research)

Gramene (www.gramene.org) is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. It launched 20 years ago and has continually grown and expanded to incorporate new tools and resources. This update by Tello-Ruiz et al. describes its…

Multi-omics analyses of wild tomato introgression lines reveal a set of gene expression-metabolite-pathogen sensitivity interactions (Nat. Genet.)

Domesticated tomato has been subjected to human selection to satisfy marketing and economic desires, leading to a loss of genetic diversity and elimination of fruits traits such as flavor, aroma and pathogen resistance. Introgression lines (ILs) that capture the genome of wild desert-adapted tomato Solanum…

Review: Less is more, natural loss-of-function mutation is a strategy for adaptation (Plant Communications)

Gene gain through duplication and gene loss through loss-of-function (LoF) mutations determine genetic variation underlying diversification and adaptive evolution. In this review, Xu and Guo highlight the importance of LoF mutations in the evolutionary success of several organisms as revealed by advancements…

Pan-genome of wild and cultivated soybeans (Cell)

Widespread genome sequencing of individuals has revealed the high level of intraspecific variability in plant species. As such, constructing high-quality pan-genomes is a growing necessity to study dynamic plant genomes. Here, Liu et al. release the soybean pan-genome formed from sequencing 2,898 accessions,…

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants (Nature Ecol. Evol.)

The green plant lineage (Viridiplantae) has long been described as having a single origin (starting with the engulfment of a cyanobacteria-like endosymbiont) that has led to two phyla: the Streptophyta, including embryophytes (land plants) and some algae such as chara and nitella, and the Chlorophyta,…

Mutation bias shapes gene evolution in Arabidopsis thaliana (bioRxiv)

Classical evolutionary theory states that the probability of a mutation occurring is independent of fitness consequences. However, reassessment of traditional assumptions is warranted with recent discoveries showing that cytogenetic (DNA sequences and epigenetic) features can affect local mutation probabilities.…

Review. The plant microbiome: From ecology to reductionism and beyond (Annu. Rev. Microbiol.)

The last two decades have witnessed tremendous progress in our understanding of plant microbiota. Fitzpatrick, Salas-González et al. highlight recent discoveries from culture-dependent and culture-independent approaches and discuss the future path towards integrating these approaches. Culture-independent…