Fernando Rodriguez Molecular - Computational Biologist

Research

Lines of Research

  1. *

    Horizontal gene transfer as a source of evolutionary innovation in metazoans

    Bdelloid rotifers carry an unusual proportion of coding sequence of non-metazoan (mostly bacterial) origin. That makes them a natural experiment in what foreign genes actually do once they are in an animal genome.

    One answer is that they can be built into the host's own regulatory systems. Bdelloids lack the canonical eukaryotic C5-methyltransferases, but encode N4CMT, an amino-methyltransferase captured from bacteria more than 60 million years ago, which deposits N4-methylcytosine at active transposons and certain tandem repeats. Another answer is chemical defense: bdelloids under attack by a fungal pathogen express horizontally acquired biosynthetic gene clusters resembling bacterial antibiotic pathways.

    Nat Commun 2022 · Nat Commun 2024 · BioEssays 2023

    Bar chart of LINE retrotransposon content and Piwi/Ago copy number across monogonont and bdelloid rotifer species, split by absence or presence of the bacterial N4CMT methyltransferase
    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.
  2. *

    Reverse-transcriptase-related genes and their biological significance

    Retroelements are far more structurally varied than the textbook categories suggest. This work characterizes Penelope-like elements (PLEs) and their relatives: an ancient clade with permuted domain architecture that turns out to be present across the green lineage and protists and to dominate many invertebrate genomes; giant reverse-transcriptase-encoding elements that reside at telomeres; and LTR retrotransposons that have captured extra open reading frames shared across otherwise distant retroelement types.

    Mol Biol Evol 2017 · Mol Biol Evol 2021 · Viruses 2017 · Mobile DNA 2013

    Two repeat landscape divergence plots for Pomphorhynchus laevis: all transposable elements in panel A, and Penelope-like elements by family in panel B, with a pie chart showing the Naiad family occupying most of the PLE content
    Landscape divergence plots showing TE activity over time and genome occupancy in the acanthocephalan Pomphorhynchus laevis. (A) All TEs, with PLEs on the top (note RepeatMasker classification as LINE/Penelope); (B) PLEs only, subdivided by families, with Naiad_Plae family (PLE/Naiad) occupying most of the space on the divergence plot and on the inserted pie chart.
  3. *

    Mobile genetic elements in sexual and ancient asexual taxa

    Theory predicts that transposable elements should behave very differently in lineages that have abandoned sex. Comparative work across bdelloid rotifers and the putatively ancient asexual ostracod Darwinula stevensoni tests that prediction against real genomes, and connects the answer to the silencing machinery, including the expansion of piRNA pathway components that target both transposable elements and foreign genes in Adineta vaga.

    eLife 2021 · Genes 2021 · Genetics 2016 · Nature 2013

    Charts showing that most protein-bound small RNAs in Adineta vaga map to transposable elements, with a strong 5-prime uridine bias and dense piRNA coverage over a TE-rich scaffold
    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.
  4. *

    Genetic transformation tools for seagrasses

    Establishing a Synthetic Biology and Genome Engineering Platform for the Marine Angiosperm Zostera marina

    Seagrasses have no established tissue culture or transformation protocols, which puts most functional genetics out of reach in these species. This work explores the initial steps toward building those tools. Several transformation strategies are being evaluated in parallel, including protoplast-based approaches, callus induction, biolistic delivery and other commonly used methods, developed alongside the foundational tissue culture protocols that are currently unavailable. The project also asks whether the monocot promoters already available are suitable for driving expression of genes of interest in seagrass transformation vectors.

    In progress

    Three panels: a researcher operating a biolistic device in a laminar flow hood, cultured seagrass shoots in a jar, and a fluorescence image of leaf cells showing green foci where particles landed
    Microprojectile bombardment under the hood.

Working with me

Undergraduate and graduate students interested in genome evolution, transposable elements, or computational approaches to comparative genomics are welcome to get in touch.

frvsbi@rit.edu CV