Entries by Facundo Romani

Widespread long-range cis-regulatory elements in the maize genome ($) (Nature Plants)

The chromatin landscape is key in the regulation of gene expression. Many studies have been made in Arabidopsis, but its genomic architecture is different to other plants. Here Ricci et al. present a very comprehensive study of chromatin analysis in maize. This work includes a huge amount of sequencing data, including ATAC-seq (transposase-accessible chromatin sequencing) […]

The prevalence, evolution and chromatin signatures of plant regulatory elements ($) (Nature Plants)

With a wide range of genome sizes and varying architectures, understanding the evolution and function of non-coding regions is not straightforward in plants. Nevertheless, many advances are coming out that will shed light on this complex scientific problem. Lu et al. performed ATAC-seq to study chromatin accessibility in 13 plant species spanning most angiosperm taxonomic […]

Genomes of subaerial Zygnematophyceae provide insights into land plant evolution ($) (Cell)

The availability of charophyte algae genomic information is helping to understand how the plant transition to a terrestrial environment occurred at the molecular level. Here, Cheng et al. are releasing two genomes from the Zygnematophyceae clade (Spirogloea muscicola and Mesotaenium endlicherianum), among the first genomes from this clade, the closest to most land plants (embryophytes). […]

Essay: Reconstructing trait evolution in plant evo–devo studies (Curr. Biol.)

Plant evo-devo studies are thriving thanks to new genetic engineering tools and the emergence of model systems such as the moss Physcomitrella patens, the liverwort Marchantia polymorpha, and the fern Ceratopteris richardii. In the past few years many debates have taken place among the community, in particular about how to draw evolutionary comparisons between species. […]

New insights into Marchantia polymorpha genome

Since the publication of the Marchantia polymorpha genome in 2017, a big update was necessary. In the past week, two groups published on improving Marchantia chromosome assembly following different experimental approaches. Diop et al. made a high-density linkage map using genetic markers obtained by ddRAD-seq, managing to assemble 88% of the genomic DNA content in […]

Early origin of miRNA-SPL module in reproductive development revealed by liverwort (Curr. Biol)

In Arabidopsis and other angiosperms, transition to flowering is controlled by a regulatory module that includes transcription factors from the SPL family and a miRNA miR156 targeting them. Marchantia and bryophytes do not make flowers, but there is an equivalent module that includes miR529c and a single target, Mp SPL2. Tsusuki et al. show here […]

Auronidins are a previously unreported class of flavonoid pigments that challenge anthocyanin biosynthesis evolved in plants (OA) (PNAS)

Plants produce pigments as a protective strategy against biotic and abiotic stress. In angiosperms, anthocyanins are the main flavonoids that play a role in this function. As the early-diverging land plant, Marchantia polymorpha also produces red pigments in response to environmental conditions, it was thought that anthocyanin biosynthesis was conserved, despite the pigment accumulated in […]

Deep conservation of cis-element variants regulating plant hormonal responses (Plant Cell)

Promoter regions upstream of transcription start sites contain DNA regulatory elements (RE) crucial for the transcriptional control of gene expression. However, REs are short degenerated sequences with low conservation during evolution. In this paper, Lieverman-Lazarovich et al. studied REs in core hormone response genes. The authors develop an alignment-free computational approach to find cases where […]

Review. Fellowship of the rings: a saga of strigolactones and other small signals (New Phytol)

Strigolactones are small signal molecules synthesized by plants. In the past few years, many studies highlighting the importance of this emerging phytohormone have been published. Strigolactones play important roles as a hormonal signals in plants and for mycorrhizal fungi interactions, they are present in all land plants, and the signaling pathways seem to be conserved. […]