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

Abstract

Background Sequencing the giga-genomes of several pine species belonging to the ancient gymnosperm clade has enabled comparative genomic analyses of these widely distributed outcrossing tree species. Initial sequence studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces. Our previous investigations revealed significant variations of class I TEs within pine subpopulations, but inoculation with pathogen induced correlated expression of TE families in pine seedlings, suggesting TE co-localisation with stress-responsive genes. 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.Results 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 were identified in both species genomes frequently inserted into genes or their flanks. The non-autonomous MITE3321 family found in gene flanking regions and provide TATA boxes, several ARR1, DOF, WRKY and GT-binding sites, which are important signals in plant transcription activation and stress-response regulation. Distribution of MITE3321 across gene non-coding regions suggests action of selective pressure on this sequences and formation of gene sub-networks, depending on the location of MITE insertions. DNA TE DTX184 could potentially form microRNAs or provide its target site, thereby connect about 200 important stress-responsive genes in both pine species. Several retrotransposons propagated in gene regions were also identified, such as Copia-1813 containing important light-responsive regulative sequences, however full-length structures of low-copy-number TEs couldn’t be verified in the current genome assemblies. Only rare gene homologs carried similar insertions, indicating that most transposition events occurred after separation of investigated pine species. Node genes that contain many types of interspersed repeats were identified and observed in multiple potential transposable element associated networks.Conclusions This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and the probability of rewiring them in 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.

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…Transcriptionally active retrotransposons can potentially participate indirectly in gene regulation and adaptation to environmental stress, since their activity is induced by stressful environmental conditions ( Belyayev et al, 2010 ; Capy et al, 2000 ; Vicient et al, 2001 ; Wessler, 1996 ). As a result, these chromosomal changes under the influence of mobile genetic elements can potentially increase the adaptive potential of specimens to stress conditions ( Belyayev et al, 2010 ; Capy et al, 2000 ; Grandbastien, 1998 ; Horvath, Merenciano & Gonzalez, 2017 ; Voronova et al, 2020 ).…”