Comparative study of pine reference genomes reveals transposable element interconnected gene networks

Angelika Voronova, Martha Rendón‐anaya, Pär Ingvarsson, Ruslan Kalendar, Dainis Ruņģis

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

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.

Original languageEnglish
Article number1216
Pages (from-to)1-29
Number of pages29
JournalGenes
Volume11
Issue number10
DOIs
Publication statusPublished - Oct 2020
Externally publishedYes

Keywords

  • Gene networks
  • Gene regulation
  • Introns
  • MITE
  • Node gene
  • Pine reference genome
  • Pinus lambertiana
  • Pinus taeda
  • Retrotransposons
  • Transposable elements

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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