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Moreno Aguilar, María Fernanda [1], Sanchez Rodriguez, Aminael [2], Arnelas Seco, Itziar [3], Catalan, Pilar [4].

Phylogenetic signal, abundance and characterization of the repeteome of the temperate Loliinae grasses.

Repetitive DNA constitutes a large percentage of most plant genomes. Subtribe Loliinae includes temperate pooid grasses from both hemispheres; some forage, pasture and lawn species are of high economic and ecological importance. Ploidy levels range from diploids to (duo) decaploids in Loliinae, and their genome sizes from 2.6 Gbp/1C to 11.8 Gbp/1C. We have used low coverage genome skimming data to identify and characterize the repeteome of several Loliinae species and to test its phylogenetic value. Skim data from 47 samples representing the main Loliinae lineages were analyzed with Repeat Explorer (RE) through the galaxy platform. Comparative analyses were performed at four evolutionary groups: Loliinae (38 species), Broad-leaved Loliinae (15), Fine-leaved Loliinae (17) and Schenodorus-Lolium (17). The genomic proportions of the repetitive elements identified by RE were used to characterize the species repeteomes. Neighbor-Joining phylogenetic trees were constructed for each repetitive element and evolutionary group using genetic distance matrices obtained from RE in R (ape package), and consensus networks of all repetitive-NJ trees were built for each group with Splitstree. ML phylogenetic trees were also constructed using the abundance values (frequencies) of each repetitive element using the Phylip package. DNA sequences of the rDNA cistron were obtained by mapping reads to a reference in Geneious and 5S rDNA sequences were extracted for each species from the RE cluster. These alignments were used to build the respective comparative ML phylogenetic trees with IQTREE. The proportion of the genome covered by the repeteome is ~ 68% on average in the Loliinae, with the diploids showing larger coverages (e. g., Lolium persicum 68%) than the polyploids (e. g., Festuca letourneuxiana 30%). The most frequent repetitive elements in Loliinae are the Ty3/gypsy/Retand and Ty1/copia/Angela retrotransposons, and the most abundant family Ty3/gypsy. By contrast, some repetitive elements are species or lineage-specific, like LTR/Gypsy/Reina present only in Lolium saxatile (0,01%) and TIR/Hat in Vulpia ciliata (0,03%). The nuclear 5S data recovered a strongly supported phylogenetic tree which was congruent with that obtained from the nuclear rDNA cistron. The repeteome-based trees retrieved similar topologies for the Schenodorus-Lolium, American I, American II, South America and Subbulbosae clades of Loliinae that those retrieved from the nuclear ribosomal genes, thus supporting the phylogenetic signal of the repetitive elements in these grasses. The Schenodorus-Lolium group showed the best resolved repeteome-topology of all Loliinae and the evolutionary positions of newly studied South African and Siberian species.

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1 - University of Zaragoza, Agricultural and Environmental Sciences, High Polytechnic School of Huesca, Ctra. Cuarte, km 1, Huesca, Huesca, 22071, Spain
2 - Universidad Tecnica Particular de Loja, Ciencias Biologicas, San Cayetano, Loja, Loja, 110101, Ecuador
3 - Universidad Técnica Particular De Loja, San Cayetanl Alto S/n, Loja, L, 11-01-608, Ecuador
4 - University of Zaragoza: Universidad de Zaragoza, Agricultural and Environmental Sciences, High Polytechnic School of Huesca, Ctra. Cuarte km 1, Huesca, Aragón, 22071, Spain

repetitive DNA
Loliinae grasses
Genome skimming
Repeat explorer
phylogenetic signal.

Presentation Type: Poster
Session: P3, Phylogenomics Posters
Location: Virtual/Virtual
Date: Wednesday, July 21st, 2021
Time: 5:00 PM(EDT)
Number: P3PL011
Abstract ID:545
Candidate for Awards:None

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