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]
![]() |
PDF
3MB |
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: |
| ||||||
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 |
Repository Staff Only: item control page