Fernando Rodriguez

Research Scientist

Fernando Rodriguez headshot
Contact Information
Education
PhD, Biology, Molecular Biology and Biochemistry Program, University of Oviedo (Spain), 2009
BS, Biology , University of Oviedo (Spain), 2002
MBL Affiliations
Bay Paul Center
Research Area
Evolution
Genomics
Lab Website
Rodriguez Lab

My research as molecular biologist lies at the junction of molecular evolution, comparative genomics and epigenetics in the field of gene silencing/activation in metazoans. During my career I have used a broad range of tools and approaches which span familiarity with population genetics, biogeography, gene evolution, comparative genomics and epigenetic regulation. I seek to address the mechanisms that eukaryotic cells can deploy in order to repress foreign genetic invasions, like transposable elements (TEs) or foreign genes acquired by horizontal gene transfer (HTG). To this point my work has focused on he role of epigenetics. Epigenetics can be defined as the study of biological mechanisms that are able to regulate gene expression and function that cannot be explained by changes in DNA sequence. These mechanisms include covalent modification of histones, DNA methylation and non-coding RNAs pathways.

At the MBL, where I have expanded my expertise in molecular biology and bioinformatic approaches, I am seeking to achieve a better understanding of epigenetic regulation in organisms, and specifically, to understand the machinery used by the host to identify and suppress unwanted visitors in the genome (like transposons and foreign genes) whose activities can be considered lethal.

Characterization of protein-bound small RNAs in A. vaga. On the left, length distribution of sRNAs mapped to annotated genomic features (TEs, CDS, UTRs, and introns). The y-axis shows combined read counts for both replicates. Right figure shows percentage of 5’-terminal nucleotides (A, T, G, and C) in each sRNA size class. The bottom right snapshot shows a genome region with small RNA coverage along a selected scaffold with full-length Vesta transposon.
Characterization of protein-bound small RNAs in A. vaga. On the left, length distribution of sRNAs mapped to annotated genomic features (TEs, CDS, UTRs, and introns). The y-axis shows combined read counts for both replicates. Right figure shows percentage of 5’-terminal nucleotides (A, T, G, and C) in each sRNA size class. The bottom right snapshot shows a genome region with small RNA coverage along a selected scaffold with full-length Vesta transposon.

 

LINE retrotransposon content (% genome) and Piwi/Ago copy numbers in 6 monogonont (green) and 10 bdelloid (blue) rotifer species. Absence or presence of bacterial HGT aminomethyltransferase (N4CMT_Av representation) in the sequenced genome is denoted on top by N4CMT- or N4CMT+, respectively. Median values are indicated by bar heights for LINE content, and by continuous orange line for copy numbers. Data points for % LINE values (+) and copy numbers (♦) are shown for all sequenced isolates from each species,
LINE retrotransposon content (% genome) and Piwi/Ago copy numbers in 6 monogonont (green) and 10 bdelloid (blue) rotifer species. Absence or presence of bacterial HGT aminomethyltransferase (N4CMT_Av representation) in the sequenced genome is denoted on top by N4CMT- or N4CMT+, respectively. Median values are indicated by bar heights for LINE content, and by continuous orange line for copy numbers. Data points for % LINE values (+) and copy numbers (♦) are shown for all sequenced isolates from each species, with number of isolates (n) in parentheses.
News and Research Highlights
Fernando Rodriguez works with
David Mark Welch Headshot
David Mark Welch
Senior Scientist and Director, Bay Paul Center
Bay Paul Center
Selected Publications

Fernando Rodriguez, Irina A. Yushenova, Daniel DiCorpo, Irina R. Arkhipova. (2022). Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nature Communications (Accepted with minor). InReview.

Rory J. Craig, Irina A. Yushenova, Fernando Rodriguez, Irina R. Arkhipova. (2021). An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes. Molecular Biology and Evolution. Oct 27;38(11):5005-5020. Pubmed.

Fernando Rodriguez, Isa Schön, Matthew Dunn, Koen Martens, Michael Shribak, Irina R. Arkhipova. (2021). A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes, 12(3), 401. Pubmed.

Reuben W Nowell , Christopher G Wilson, Pedro Almeida, Philipp H Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodriguez, Irina R Arkhipova, Timothy G Barraclough. (2021). Evolutionary dynamics of transposable elements in bdelloid rotifers. Elife Feb 5;10:e63194. Pubmed.

Olga A. Vakhrusheva, Elena A. Mnatsakanova, Yan R. Galimov, Tatiana V. Neretina, Evgeny S. Gerasimov, Sergey A. Naumenko, Svetlana G. Ozerova, Arthur O. Zalevsky, Irina A. Yushenova, Fernando Rodriguez, Irina R. Arkhipova, Aleksey A. Penin, Maria D. Logacheva, Georgii A. Bazykin & Alexey S. Kondrashov. (2020). Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nature Communications volume 11, Article number: 6421. Pubmed.

Fernando Rodriguez and Irina R. Arkhipova. Transposable elements and polyploid evolution in animals (2018). Current Opinion in Genetics & Development. 49:115-123. Pubmed.

Arkhipova IR, Yushenova IA, Rodriguez F. (2017) Giant reverse transcriptase-encoding transposable elements at telomeres. Mol Biol Evol. 34(9):2245-2257. Pubmed.

Rodriguez F, Arkhipova I. (2016). Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga. Genetics. 203(1):255-268. Pubmed. Selected article in Genetics Spotlight 2016.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.(2013). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 500:453-457. Pubmed.

Rodriguez F, Pérez T, Hammer S, Albornoz J, Domínguez A. (2010). Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra). BMC Evolutionary Biology. 10:222. Pubmed.