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

Angelika Voronova1, Martha Rendón-Anaya2, Pär Ingvarsson2

  • 1Genetic Resource Centre, Latvian State Forest Research Institute "Silava", LV2169 Salaspils, Latvia.

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|October 21, 2020
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Summary

Transposable elements (TEs) in pine genomes are abundant in gene regions, especially introns of stress-responsive genes. This suggests TEs play a role in adaptive environmental responses in pine populations.

Keywords:
MITEPinus lambertianaPinus taedagene networksgene regulationintronsnode genepine reference genomeretrotransposonstransposable elements

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Conifer genomes, particularly pines, are characterized by large intergenic regions rich in transposable elements (TEs).
  • Understanding TE distribution is crucial for comparative genomics and evolutionary studies in outcrossing tree species.

Purpose of the Study:

  • To analyze the distribution of TEs within gene regions of *Pinus taeda* and *Pinus lambertiana* genomes.
  • To identify TE families and sequence motifs potentially involved in gene regulation and network formation.
  • To investigate the relationship between TEs and stress-responsive genes in pines.

Main Methods:

  • Comparative genomic analysis of assembled *Pinus taeda* and *Pinus lambertiana* genomes.
  • High-performance computing for analyzing large genomic datasets.
  • Identification and characterization of transposable element families and their insertion sites within gene regions.

Main Results:

  • Several TE families were found to frequently insert into or near genes in both pine species.
  • Identified sequence motifs within TEs may facilitate binding of regulatory factors, influencing transcription initiation.
  • TEs showed increased accumulation in introns of stress-responsive genes, suggesting a role in adaptive responses.

Conclusions:

  • Transposable elements are actively involved in gene regulation and network formation in pine genomes.
  • The accumulation of TEs in stress-responsive gene introns points to their contribution to adaptive environmental responses in pine populations.
  • Genome annotation quality significantly impacts the investigation of TEs and their functional roles.