In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

Abstract

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55–83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

Obtaining retrotransposon sequences, analysis of their genomic distribution and use of retrotransposon-derived genetic markers in lentil (Lens culinaris Medik.)

“…In lentil the Ty1-copia , Ty3-gypsy and TRIM family frequencies are respectively 17.6%, 78.7% and 0.03% of the LTR-RTs [9]. The different lineage estimations obtained by our in silico search agree with these figures.…”

TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads

“…These clusters were manually annotated during our previous study (30) and included 174 satellites; the remaining clusters represented other kinds of genomic repeats. The C and P values of these clusters were used as training data for discriminant analysis to find the best model for satellite prediction (Figure 2A).…”

Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

“…In addition to proving this mechanism by detecting various stages of the retroelement array expansions in the nanopore reads, the present work on L. sativus is the first in which this phenomenon was found to be responsible for the emergence of so many different satellites within a single species. Considering the widespread occurrence and high copy numbers of Tat/Ogre elements in many plant taxa (Neumann et al, 2006;Kubát et al, 2014;Macas et al, 2015), it can be expected that they play a significant role in satDNA evolution by providing a template for novel satellites that emerge by the expansion of their short tandem repeats. Additionally, similar tandem repeats occur in other types of mobile elements; thus, this phenomenon is possibly even more common.…”