Comparative genome-wide analysis of repetitive DNA in the genus Populus L.

Abstract

Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novak et al. 2010). The repetitive portion of the genome ranged from 33.8 in P. nigra to 46.5% in P. tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7 : 1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeats types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analyzed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving.

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

“…This number has been surpassed by a recent study where 164 satDNA families have been identified in Teleostei fish, being this the biggest satellitome characterized for a given species so far [70]. The availability of a methodology capable of assessing satDNA array abundance and diversity led to an explosion of comparative studies across a wide range of clades, including mammals, insects and plants (e.g., [44,45,69,[71][72][73]) providing insights into these sequences.…”

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

“…Gag genes are generally the most variable LTR retrotransposon domains, even if they encode a major structural protein [37,48], and are responsible for the packaging of retrotransposon RNA and proteins [49]. The polyprotein gene encodes some enzymatic domains such as the aspartic proteinase ( AP ), reverse transcriptase ( RT ), RNase H [50], and integrase ( INT ) [51,52,53]. Each domain has a specific role in the replication cycle [54] (Table 1).…”

“…Each domain has a specific role in the replication cycle [54] (Table 1). In some cases, they have another region upstream the 3′ LTR called chromodomain that can be responsible for targeted integration [38,52,55] and for escaping silencing by the specific targeting of heterochromatic regions [55].…”

“…One of the most interesting impacts that TEs could have on the host genomes and phenotypes [83] is the alteration of gene activity [52]. These impacts can include the imposition of intragenomic selection pressures through their effects on gene expression [76], inactivation of coding or regulatory regions of the gene [124], mutations that change the protein sequence, variation of the pattern of expression or alternative splicing [3], alteration of the expression of neighboring genes by epigenetic effects [82], or through modification of transcription factor expression [151], redirection of stress stimuli to adjacent genes [9], and the influence on the conservation, rearrangement, and deletion of gene pairs [152].…”

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

“…LTR-REs can be classified into two major superfamilies, Gypsy and Copia [19], depending on the order of the enzyme-coding regions within the Pol domain. Superfamilies, on their turn, are subdivided into a number of lineages in relation to their structure and sequence [23][24][25][26][27][28][29].…”