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 Affiliation
Bay Paul Center
Research Area
Evolution
Genomics
Lab Website

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鈥-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.听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.听Right figure shows percentage of 5鈥-terminal nucleotides (A, T, G, and C) in each sRNA size class.听The bottom right snapshot shows a genome region with small RNA coverage along a听selected听scaffold with听full-length听Vesta transposon.

听

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 (鈾) 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)听rotifer听species.听Absence or presence of bacterial HGT aminomethyltransferase (N4CMT_Av representation) in the听sequenced听genome is denoted on top by N4CMT- or N4CMT+, respectively.听Median values are indicated by bar heights听for LINE content, and by continuous orange line for copy numbers. Data points for听% LINE values (+) and copy numbers (鈾) 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).听.

Rory J. Craig, Irina A. Yushenova,听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.听.

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

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

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,听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.听.

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

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

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

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barth茅l茅my 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,听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听Adineta vaga. Nature. 500:453-457.听.

Rodriguez F, P茅rez T, Hammer S, Albornoz J, Dom铆nguez A. (2010). Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus听Rupicapra). BMC Evolutionary Biology. 10:222.听.