Publications

Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA

Peredo EL, Kulp R, Rodriguez F, Weintraub MN, Anand M, Bixler S, Koller J, Lee C, Mathai D, Tuytschaevers S, Kumar G

Microbiology Resource Announcements e00380-26

doi:10.1128/mra.00380-26

Bdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen

Nowell RW, Rodriguez F, Hecox-Lea BJ, Mark Welch DB, Arkhipova IR, Barraclough TG, Wilson CG

Nature Communications 15:5787

doi:10.1038/s41467-024-49919-1

Shaping eukaryotic epigenetic systems by horizontal gene transfer Review

Arkhipova IR, Yushenova IA, Rodriguez F

BioEssays 45(7):e2200232

doi:10.1002/bies.202200232 PDF

An overview of best practices for transposable element identification, classification, and annotation in eukaryotic genomes Chapter

Rodriguez F, Arkhipova IR

In: Branco MR, de Mendoza Soler A (eds), Transposable Elements. Methods in Molecular Biology, vol. 2607. Humana, New York, NY

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Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA

Rodriguez F, Yushenova IA, DiCorpo D, Arkhipova IR

Nature Communications 13:1072

doi:10.1038/s41467-022-28471-w PDF

Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

Darras H, De Souza Araujo N, Baudry L, Guiglielmoni N, Lorite P, Marbouty M, Rodriguez F, Arkhipova I, Koszul R, Flot JF, Aron S

Peer Community Journal 2:e40

doi:10.24072/pcjournal.140 PDF

An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes

Craig RJ, Yushenova IA, Rodriguez F, Arkhipova IR

Molecular Biology and Evolution 38(11):5005-5020

doi:10.1093/molbev/msab225 PDF

A survey of transposon landscapes in the putative ancient asexual ostracod Darwinula stevensoni

Schön I, Rodriguez F, Dunn M, Martens K, Shribak M, Arkhipova IR

Genes 12(3):401

doi:10.3390/genes12030401 PDF

Evolutionary dynamics of transposable elements in bdelloid rotifers

Nowell RW, Wilson CG, Almeida P, Schiffer PH, Fontaneto D, Becks L, Rodriguez F, Arkhipova IR, Barraclough TG

eLife 10:e63194

doi:10.7554/eLife.63194 PDF

Editorial: Mobile elements and plant genome evolution, comparative analyzes and computational tools Editorial

Kalendar R, Sabot F, Rodriguez F, Alix K, Natali L, Karlov GI

Frontiers in Plant Science 12:735134

doi:10.3389/fpls.2021.735134 PDF

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS

Nature Communications 11:6421

doi:10.1038/s41467-020-19614-y PDF

A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum

Nedoluzhko AV, Sharko FS, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG

PLOS ONE 14(12):e0226485

doi:10.1371/journal.pone.0226485 PDF

Transposable elements and polyploid evolution in animals Review

Rodriguez F, Arkhipova IR

Current Opinion in Genetics & Development 49:115-123

doi:10.1016/j.gde.2018.04.003 PDF

Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus

Pérez T, Rodriguez F, Fernández M, Albornoz J, Domínguez A

Gene 628:63-71

doi:10.1016/j.gene.2017.07.035 PDF

Giant reverse transcriptase-encoding transposable elements at telomeres

Arkhipova IR, Yushenova IA, Rodriguez F

Molecular Biology and Evolution 34(9):2245-2257

doi:10.1093/molbev/msx159 PDF

LTR-retrotransposons from bdelloid rotifers capture additional ORFs shared between highly diverse retroelement types

Rodriguez F, Kenefick AW, Arkhipova IR

Viruses 9(4):78

doi:10.3390/v9040078 PDF

Multitasking of the piRNA silencing machinery: targeting transposable elements and foreign genes in the bdelloid rotifer Adineta vaga

Rodriguez F, Arkhipova IR

Genetics 203(1):255-268

Selected for the 2016 GENETICS Spotlight

doi:10.1534/genetics.116.186734 PDF

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

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

Nature 500:453-457

doi:10.1038/nature12326 PDF

Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families

Arkhipova IR, Yushenova IA, Rodriguez F

Mobile DNA 4:19

doi:10.1186/1759-8753-4-19 PDF

Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids Review

Arkhipova IR, Rodriguez F

Cytogenetic and Genome Research 140(2-4):295-311

doi:10.1159/000352069 PDF

Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra)

Rodriguez F, Pérez T, Hammer S, Albornoz J, Domínguez A

BMC Evolutionary Biology 10:222

doi:10.1186/1471-2148-10-222 PDF

Cytochrome b phylogeography of chamois (Rupicapra spp.): population contractions, expansions and hybridizations governed the diversification of the genus

Rodriguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Martinkova N, Albornoz J, Domínguez A

Journal of Heredity 100(1):47-55

doi:10.1093/jhered/esn074 PDF

Cytochrome b pseudogene originated from a highly divergent mitochondrial lineage in genus Rupicapra

Rodriguez F, Albornoz J, Domínguez A

Journal of Heredity 98(3):243-249

doi:10.1093/jhered/esm013 PDF

Multitasking of the piRNA silencing machinery: targeting transposable elements and foreign genes in the bdelloid rotifer Adineta vaga Feature

Rodriguez F, Arkhipova IR

GENETICS Spotlight 2016, Genes to Genomes

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El rebeco cantábrico, filogeografía e historia evolutiva Chapter

Domínguez Sanjurjo A, Rodriguez Vazquez F, Albornoz Pons J, Pérez Méndez T

In: Pérez-Barbería FJ, Palacios B (eds), El Rebeco Cantábrico (Rupicapra pyrenaica parva): Conservación y gestión de sus poblaciones. Colección Naturaleza y Parques Nacionales, Serie Técnica

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Cytochrome b phylogeography of chamois (Rupicapra spp.): population contractions, expansions and hybridizations characterize the diversification of the genus Abstract

Rodriguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Martinkova N, Albornoz J, Domínguez A

82nd Annual Meeting of the German Society of Mammalogy, Vienna. Mammalian Biology 73[Suppl. 1]:16

Beef traceability based on DNA fingerprinting Article

Domínguez A, Rodriguez F

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