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. 2020 Oct 16;11(10):1216.
doi: 10.3390/genes11101216.

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

Angelika Voronova  1 , Martha Rendón-Anaya  2 , Pär Ingvarsson  2 , Ruslan Kalendar  3 , Dainis Ruņģis  1
Affiliations

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

Angelika Voronova et al. Genes (Basel). .

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.

Keywords: MITE; Pinus lambertiana; Pinus taeda; gene networks; gene regulation; introns; node gene; pine reference genome; retrotransposons; transposable elements.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Comparison of TE distribution in gene non-coding regions of high-quality genes of the P. lambertiana genome v.1.01 (PILA) and filtered annotated gene set of P. taeda v.2.0 (PITA).
Figure 2
Figure 2
Distribution of >1 kb hits to TEs in gene introns of filtered P. taeda (PITA) genes and high-quality P. lambertiana (PILA) genes.
Figure 3
Figure 3
(A) Distribution of Plater MITE insertions across P. taeda (PITA) and P. lambertiana (PILA) gene-flanking regions. (B) Distribution of Plater MITE insertions across P. taeda (PITA) and P. lambertiana (PILA) gene introns. World cloud generated from biological process GO terms of P. taeda genes involved in the networks using the online tool https://wordart.com/. (C) Alignment of P. taeda (PITA) and P. lambertiana (PILA) consensus sequences with predicted plant cis-acting regulatory elements.
Figure 4
Figure 4
Gene network formed by Irbe DNA TE presence in the gene introns of P. taeda v.2.0.
See this image and copyright information in PMC

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References

    1. Zhou H., Liu Q., Li J., Jiang D., Zhou L., Wu P., Lu S., Li F., Zhu L., Liu Z., et al. Photoperiod-and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res. 2012;22:649–660. doi: 10.1038/cr.2012.28. - DOI - PMC - PubMed
    1. Zhao X., Li J., Lian B., Gu H., Li Y., Qi Y. Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nat. Commun. 2018;9:5056. doi: 10.1038/s41467-018-07500-7. - DOI - PMC - PubMed
    1. Lee H., Zhang Z., Krause H.M. Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners? Trends Genet. 2019;35:892–902. doi: 10.1016/j.tig.2019.09.006. - DOI - PubMed
    1. McClintock B. The significance of responses of the genome to challenge. Science. 1984;226:792–801. doi: 10.1126/science.15739260. - DOI - PubMed
    1. Wessler S.R. Plant retrotransposons: Turned on by stress. Curr. Biol. 1996;6:959–961. doi: 10.1016/S0960-9822(02)00638-3. - DOI - PubMed

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