Happy to see our paper “SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes” published in Frontiers in Genetics! A robust CNV simulator for exome data was sorely needed, and we think SECNVs is filling this gap nicely. We included a number of options in this tool that will help customize CNV and exome read simulations to test current and novel algorithms to detect CNVs.

It was a pleasure working with co-authors Yue Xing, Alan Dabney, Xiao Li, Guosong Wang and Clare Gill on this project. Yue Xing, who was a PhD student in the Genetics program when we started this work, deserves a lot of credit for her contribution to this work.

Super excited to see this very nice feature on de novo genes by Adam Levy in Nature! It was a lot of fun and a privilege to talk to Adam about de novo genes a few months ago. Also, Science published a Feature on microproteins that is relevant to DNGs. Amazing to see the progress that has been made in this field in recent years!

 

Several authors have found that gymnosperms, including Pinaceae, share a low substitution rate compared to angiosperms. In contrast, we report this paper a remarkable high level of gene turnover (the sum of gene duplication and gene loss events) in Pinaceae. We also show how gene turnover rates can be reliably estimated when gene annotation is still preliminary, as is the case in sequenced Pinaceae genomes. Kudos to former postdoc Tomasz Koralewski for his fundamental contribution to this study!

 

 

Our collaborative study on the Douglas-fir genome paper is now published online in G3! Postdoc Tomasz Koralewski and I contributed with the analysis of gene family evolution in DF and other Pinaceae. Lots of interesting results came from this work, for instance: Pinaceae shows a comparable if not higher gene turnover rate than angiosperms (when polyploidization is not taken into account), some genetic networks expanded in DF, including the interesting pathway involved in jasmonate regulation, and most nuclear genes in the plastid ndh complex were lost across Pinaceae.

    

IBC amazing venue                                              Jingjia Li’s poster at IBC

During my talk at IBC

 

Lots of traveling to great scientific meetings in June and July this year.

In June 19-22 I was in the lovely Melbourne, FL, to present our work on gene turnover rates at the 34th Southern Forest Tree Improvement Conference. It was a great opportunity to learn more about ongoing work in applying genetics and genomics to tree improvement. Also, it never hurts to be at a conference on the beach, although one can’t help but wondering about the impact of miles of resorts on a barrier island, particularly for the nesting activity of sea turtles.

A very difference meeting took place the first week of July in Austin. Postdoc Tomasz Koralweski and I traveled to our state capital to present two posters on convergent evolution in C4 grasses and in marine mammals (!) at the Annual Meeting of the Society of Molecular Biology and Evolution. The SMBE’s is one of my favorite meetings, and this year’s program was certainly not disappointing (program here). I cannot simply summarize the astonish amount of science that I have witnessed those 4 days, nor point to any specific highlight. It was great though to get some feedback about our current research, and to get inspired by some of the talks and posters we have seen.

Finally, at the end of July I traveled to Shenzhen, China, for the XIX International Botanical Congress. Almost 7,000 (!!) scientists convened to the South-eastern Chinese megacity, which was mostly built in the past 30 years across the border with Hong Kong, to discuss about anything botanical. IBC is a unique event, held every six years–the very first IBC was in Paris in 1900, although the conference stems from horticulture and botanical annual meetings that took place the first time in Brussels in 1864! It was quite an honor to give a short talk at IBC, even though it was the last talk of the last day. As usual with talks, it gave me the chance to re-think and improve our work on gene turnover rates in Pinaceae. Now we are wrapping up the paper–hopefully it will see the light later this year.

Jingjia Li, graduate student in the CasolaLab, also attended IBC and presented here work on the transcriptomic analysis of drough-tolerance in loblolly pine!

More info on the IBC can be found in the AoBBlog by Pat Heslop-Harrison and in the very detailed posts on Jeff Ollerton’s Biodiversity Blog (July 2017)

 

Esther Betrán and I wrote a review on the molecular mechanisms and evolutionary consequences of a marvelous byproduct of genome infestation by retroelements: gene retroposition. This is a quite long account, yet a surely incomplete one, of the astonishing discoveries made in the past 30+ years on how retrogenes and other retrocopies originate, change and affect genome evolution. And yet, so many questions remains unanswered in this field, or have been explored in depth only in a few model organisms. Luckily, this is  a very active area in evolutionary genomics: at least six more papers on retrogenes were published since the beginning of this year. Our group is also working on retrogenes in conifers, a taxonomic group with a lot of retroelements but no work yet addressing their impact in terms of gene retroposition. I hope to post soon about this project as well!

Casola C, Betrán E “The genomic impact of gene retrocopies: what have we learned from comparative genomics, population genomics and transcriptomic analyses?” Genome Biology and Evolution. 2017 Jun 12

 

I am very pleased to welcome two new graduate students in our lab!

Jingjia Li has joined the ESSM graduate program as a Ph.D. student to study the genetic basis of drought resistance in loblolly pine.

Weixi Zhu will work on the pseudogenes evolution in conifers during his Master studies in the MEPS program.

You can see new and old lab recruits standing in awe in front of the magnificent section of a redwood tree born sixteen years before Columbus’ first voyage to the New World

(photo by Mengmeng Lu)