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

Voronova, Angelika and Rendón Anaya, Martha and Simone, Domenico and Kalendar, Ruslan and Rungis, Dainis (2020). Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes. 11 , 1216
[Research article]

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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.

Authors/Creators:Voronova, Angelika and Rendón Anaya, Martha and Simone, Domenico and Kalendar, Ruslan and Rungis, Dainis
Title:Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks
Series Name/Journal:Genes
Year of publishing :2020
Volume:11
Article number:1216
Number of Pages:28
Publisher:MDPI
ISSN:2073-4425
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Genetics (medical genetics to be 30107 and agricultural genetics to be 40402)
Keywords:pine reference genome, gene networks, gene regulation, node gene, transposable elements, retrotransposons, MITE, Pinus taeda, Pinus lambertiana, introns
URN:NBN:urn:nbn:se:slu:epsilon-p-109316
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-109316
Additional ID:
Type of IDID
DOI10.3390/genes11101216
Web of Science (WoS)000586180400001
ID Code:19763
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:22 Dec 2020 20:23
Metadata Last Modified:15 Jan 2021 19:47

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