Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses

Minaya, Miguel; Pimentel, Manuel; Mason‐Gamer, Roberta J.; Catalán, Pilar

doi:10.1016/j.ympev.2013.03.005

Cited by 16 publications

(29 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Lian et al, 2013), but could also be related to other unknown biological or evolutionary processes (cf. Minaya et al, 2013). Most of the potential parental sequences for the detected recombinants are phylogenetically close.…”

Section: Beta-amylase Phylogenymentioning

confidence: 97%

“…While alignment was generally straightforward in the coding regions, there were some intron regions where patterns of length variation made homology assessment difficult. We also found a Miniature Inverted repeat Transposable Element (MITE) in intron 4, which included highly variable and non-homologous transposable elements and their footprints (Minaya et al, 2013). Seven regions with ambiguous alignments and/or MITEs were excluded from subsequent analyses [ Supplementary Fig.…”

Section: Taxon Sampling and Dna Analysismentioning

confidence: 99%

“…The Poaceae cpDNA-ITS tree (cf. Minaya et al, 2013) was constructed using the multicopy ribosomal ITS1-5.8S-ITS2 region and the plastid matK, ndhF, trnTL, and trnLF regions from a collection of 142 grass taxa plus the close relative Joinvillea (Joinvillaceae) included as an outgroup (Table S1). Published primers and protocols were used to amplify and sequence the ITS, trnTL, and trnLF regions Quintanar et al, 2007), the ndhF gene (Catalán et al, 1997), and the matK gene (Döring et al, 2007).…”

Section: Species Tree Reconstructionmentioning

confidence: 99%

“…2) and the detection of various MITEs (Minaya et al, 2013) highlight the frequent occurrence of evolutionary events that violate the assumption that phylogenetic history is strictly tree-like, such as recombination, relaxed selection pressure, semiparalogy, incomplete lineage sorting, horizontal gene transfer, or differential gene copy losses in the b-amylase gene. Thus, b-amylase gene sequences should be applied to phylogenetic analyses with caution.…”

Section: Phylogenetic Signals Of B-amylase Sequences Within the Pooideaementioning

confidence: 99%

“…Phylogenies based on molecular data help us to understand a variety of genomic evolutionary phenomena such as pseudogenization, gene duplication (paralogy), lineage sorting, recombination, transposition, and horizontal gene transfer (Mason-Gamer and Soreng and Davis, 2000;Catalán et al, 2004;Minaya et al, 2013). These evolutionary events can result in a phylogenetic history that is more reticulate than bifurcating (cf.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

Minaya

Díaz-Pérez

Mason‐Gamer

et al. 2015

Molecular Phylogenetics and Evolution

Self Cite

View full text Add to dashboard Cite

Section: Beta-amylase Phylogenymentioning

confidence: 97%

Section: Taxon Sampling and Dna Analysismentioning

confidence: 99%

Section: Species Tree Reconstructionmentioning

confidence: 99%

Section: Phylogenetic Signals Of B-amylase Sequences Within the Pooideaementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

Minaya

Díaz-Pérez

Mason‐Gamer

et al. 2015

Molecular Phylogenetics and Evolution

Self Cite

View full text Add to dashboard Cite

Morphological and phylogenetic evidence for subtribe Cinninae and two new subtribes, Hookerochloinae and Dupontiinae (Poaceae tribe PoeaePPAMclade)

Gillespie

Soreng

Bull

et al. 2022

TAXON

View full text Add to dashboard Cite

Molecular phylogenetic analyses and morphological characters of the grass supersubtribe Poodinae (tribe Poeae, PPAM clade) were evaluated with the goal of determining the relationships of single-flowered spikelet genera recently classified in subtribe Cinninae and the sister genus of the New Zealand endemic genus Simplicia. A total of 136 samples representing 40 genera and 105 species were analyzed for three plastid (matK, trnC-rpoB, trnT-trnL-trnF) and two nuclear ribosomal DNA markers (ITS, ETS). The Cinninae subtribe, including Aniselytron, Cinna, Cinnastrum, Cyathopus, and Simplicia, was recovered as monophyletic with weak support only in the combined analysis with known/putative hybrid taxa removed. Cinna (excluding Cinnastrum) resolved as paraphyletic due to the position of the morphologically distinctive Cyathopus. Cinninae are characterized by flat leaf blades, open panicles, small, strongly compressed, single-flowered spikelets, with a rachilla extension, and lemmas that are awnless or with a short subterminal awn. The genus Cinnastrum is resurrected for Cinna poiformis and differs from Cinna in its broader glumes and subterete caryopsis with solid endosperm. Simplicia is likely most closely related to the southern and eastern Asian genus Aniselytron, with which it shares unequal and short lower glumes and spikelet disarticulation above the glumes, in contrast to the other three genera of the subtribe. The HSAQN clade, which has mainly multi-flowered spikelets and is sister to Cinninae, is named subtribe Hookerochloinae, including Arctagrostis, Hookerochloa, Nicoraepoa, Saxipoa, and Sylvipoa. The DAD clade, which is known to be of reticulate origin postulated here as involving Cinninae, is named subtribe Dupontiinae, and includes Arctohyalopoa, Arctophila, Dupontia, and Dupontiopsis. These three subtribes, together with subtribes Alopecurinae, Beckmanniinae, and Ventenatinae (along with Brizochloinae not tested here), make up the well-supported Alopecurinae superclade within supersubtribe Poodinae.

show abstract

Diversification of fescues (Festuca sect. Eskia, Poaceae), a key‐component of southern European mountainous grasslands

Mucko,

Lakušić,

Frajman

et al. 2024

TAXON

View full text Add to dashboard Cite

Grasslands cover approximately 30% of all land area and represent one of the most extensive and diverse ecosystems of the world. One of the largest globally distributed genera dominating various types of grasslands is Festuca (Loliinae, Poaceae). In this study, we disentangle the origin and diversification of early divergent lineages within fine‐leaved (FL) Loliinae, namely F. sect. Eskia and F. sect. Dimorphae (Eskia‐Dimorpha Group). We inferred phylogenetic relationships among 218 populations of 129 Loliinae taxa using nuclear ribosomal ITS and plastid trnT‐trnF sequences. Relative genome size (RGS) and ploidy level estimations revealed multiple polyploidisations within F. sect. Eskia. We uncovered previously unknown tetraploid and hexaploid populations of different species from the Balkan Peninsula. The inferred phylogenies revealed the sequential divergence of Eskia‐Dimorpha Group lineages in the early evolution of FL Loliinae, but also incongruences in the position as well as the composition of different clades between the nuclear and plastid‐based trees. Despite incongruences, some well‐supported and geographically segregated clades of single or closely related species from the Alps, the Pyrenees or the Balkan Peninsula were resolved. The most pronounced discordance between the plastid and nuclear data were among several taxa endemic to the Balkan Peninsula. Our data suggest that genome downsizing followed polyploidisation and that evolutionary dynamics of RGS‐ups and downs within F. sect. Eskia were strongly phylogenetically correlated. Overall, our study underscores the intricate evolutionary history and differentiation of species within the Eskia‐Dimorpha Group, emphasizing the need for further research to refine phylogenetic hypotheses and taxonomic circumscriptions, thereby enhancing our understanding of grassland biodiversity and evolution.

show abstract

Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses

Cited by 16 publications

References 76 publications

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal

Morphological and phylogenetic evidence for subtribe Cinninae and two new subtribes, Hookerochloinae and Dupontiinae (Poaceae tribe PoeaePPAMclade)

Diversification of fescues (Festuca sect. Eskia, Poaceae), a key‐component of southern European mountainous grasslands

Contact Info

Product

Resources

About