A genomic survey of LINE elements in Pipidae aquatic frogs shed light on Rex-elements evolution in these genomes

Gama, Joana de Moura; Ludwig, Adriana; Gazolla, Camilla Borges; Guizelini, Dieval; Recco‐Pimentel, Shirlei Maria; Bruschi, Daniel Pacheco

doi:10.1016/j.ympev.2022.107393

Cited by 2 publications

(1 citation statement)

References 90 publications

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“…Poorly aligned sequences were removed from the alignment using TrimaAl ( -resoverlap 0.75 -seqoverlap 80). Because of the short RT domain, the deep divergence time of LINE superfamilies, and the consequently difficulties in identifying stable LINE phylogenies (e.g., [ 29 , 30 , 106 ]), we used a combination of neighbor-joining, unconstrained maximum likelihood (ML), and constrained ML tree inferences. Each topology was then statistically tested in a ML framework to produce a confident phylogeny useful for LINE classification.…”

Section: Methodsmentioning

confidence: 99%

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Martelossi,

Nicolini,

Subacchi

et al. 2023

BMC Biol

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Background Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. Results We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. Conclusions We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a “stealth drivers” model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.

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Section: Methodsmentioning

confidence: 99%

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Martelossi,

Nicolini,

Subacchi

et al. 2023

BMC Biol

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Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae)

et al. 2023

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Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events — one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.

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A genomic survey of LINE elements in Pipidae aquatic frogs shed light on Rex-elements evolution in these genomes

Cited by 2 publications

References 90 publications

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution

Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs (Xenopus, Pipidae)

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