Tag Archives: Plantbiology

Welcome back on atcgeek. Now from Barcelona.

I have written this post over and over, any time ending up quite a lot disappointed about the result. If you quit writing for a while, starting back off is all but easy. But the reason why I suspended my blogging during the last month is really worthwhile, as my life changed radically, and I needed time to figure anything out. I have now moved from Rome to Barcelona, awarded with a PhD fellowship at the Centre for Research in Agricultural Genomics (CRAG), a pretty unique center in its kind, involving tens of groups working on all the shades of plant biology, and included in the amazing framework of the Autonomous University of Barcelona Science Park. My project, supervised by Josep Casacuberta, will investigate the role of transposable elments in phenotype determination, and I am already loving it.


During the last quarter of 2014, I saw the interest in this silly diary slightly, but steadly growing and, along with my best wishes for a bright 2015, I want to thank anyone who appreciated my blog, the ones who shared nice comments, and the ones who criticized my work, whose contribution to my personal growth is always fundamental.


I will back to the usual writing very soon, with the hope to enjoy further good discussions with commenters, and to learn somenthing from them. So, happy 2015 from Barcelona, and let’s keep in touch.

The role of cis-regulatory sequences in Zea mays evolution.

The paper I am going to share today collected my attention because it merges two fundamental topics that are quite a lot undertaken in evolutionary biology: plant genomics and the rule of cis-regulatory elements in evolution. Plant biology provides an excellent framework to perform studies in genomic evolution. Even if the knowledge acquired is applied mostly in agricultural biotechnology,  that is a field that trills me a lot, plants represent a perfect environment to understand general- validity principles in genomic evolution. The role of cis- regulatory elements, and their contribution to organism differentiation, are generally understood to be very relevant, but I sense that this topic is quite neglected and a bit obscure.

Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. (Lemmon et al., Plos Genetics, 2014)

That is why I have particularly enjoyed the reading of this brand new paper, authored by Zachary H. Lemmon and co-workers, and developed in a collaboration between the University of Wisconsin and Ithaca University (NY). In plant biology, one of the main points of interest is obviously the process of domestication, and its analysis under a molecular point of view. In this paper, maize domestication is analyzed by a genomic comparison among domesticated  and non domesticated species within the Zea genus.

To examine the differences in gene regulation during maize domestication from its wild progenitor, teosinte, an allele specific expression analysis is performed on pure lineages and hybrids in different trans and cis regulatory regimes. The investigation focuses on three tissues (ear, leaf and stem) from different developmental stages. RNA-seq analysis provide the confirmation of the consistent cis regulatory divergence in genes that are significantly correlated with the ones under selection during domestication and crop improvement. This suggests the important role for cis regulatory elements in maize evolution.

As the authors argue the relevance of this result for plant biology, we can understand that this study highlights the importance of regulatory genome in evolution, and the great potential that plant biology have as framework for evolutionary biology.