Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks.

Angelika Voronova,Pär Ingvarsson,Martha Rendón-Anaya,Dainis Ruņģis,Ruslan Kalendar

doi:10.3390/genes11101216

Abstract

Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.

Highlights

The functional role of transposable element (TE) insertions distributed throughout plant genomes is less studied and phenotypic changes are less obvious compared with protein-coding regions [1,2,3].Transposition of transposable elements (TEs) is linked to stress conditions and evolutionary change [3,4,5,6,7,8,9,10,11,12], but these sequences are usually controlled by the host organism [13]
RLXs proliferate via RNA transcript intermediates, but DNA transposons excise from their current location and migrate to a new genomic locus
The quality of reference genomes and the repeat database used play a major role when analyzing the presence of TEs in gene regions

Summary

Introduction

The functional role of transposable element (TE) insertions distributed throughout plant genomes is less studied and phenotypic changes are less obvious compared with protein-coding regions [1,2,3].Transposition of TEs is linked to stress conditions and evolutionary change [3,4,5,6,7,8,9,10,11,12], but these sequences are usually controlled by the host organism [13]. The functional role of transposable element (TE) insertions distributed throughout plant genomes is less studied and phenotypic changes are less obvious compared with protein-coding regions [1,2,3]. The most prevalent TEs in plants are long terminal repeat (LTR) retrotransposons (RLXs), which are sequences that contain direct repeats that flank the internal sequence or body of the element. The internal region of autonomous RLXs contain gagand polyprotein-coding domains that produce the proteins necessary for retrotransposition, namely, protease, reverse transcriptase, and integrase. Some non-autonomous DNA transposons have been found more frequently in plant gene regions, such as Miniature Inverted-repeat Transposable Elements (MITEs) [46,47,48]. Distributed TE families are broadly used as molecular markers in population genetic investigations and marker-assisted breeding [48,49,50,51,52,53,54,55,56,57]

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