Repeated evolution of heat responsiveness among Brassicaceae COPIA transposable elements

Eukaryotic genomes contain repetitive DNA sequences. This includes simple repeats and more complex transposable elements (TEs). Many TEs reach high copy numbers in the host genome, owing to their amplification abilities by specific mechanisms. There is growing evidence that TEs contribute to gene transcriptional regulation. However, excess of TE activity may lead to reduced genome stability. Therefore, TEs are suppressed by the transcriptional gene silencing machinery via specific chromatin modifications. In contrary, effectiveness of the epigenetic silencing mechanisms imposes risk for TE survival in the host genome. Therefore, TEs may have evolved specific strategies for bypassing epigenetic control and allowing the emergence of new TE copies. Recent studies suggested that the epigenetic silencing can be, at least transiently, attenuated by heat stress in A. thaliana. Heat stress induced strong transcriptional activation of COPIA78 family LTR-retrotransposons named ONSEN, and even their transposition in mutants deficient in siRNA-biogenesis. ONSEN transcriptional activation was facilitated by the presence of heat responsive elements (HREs) within the long terminal repeats, which serve as a binding platform for the HEAT SHOCK FACTORs (HSFs). This thesis focused on the evolution of ONSEN heat responsiveness in Brassicaceae. By using whole-transcriptome sequencing approach, multiple Arabidopsis lyrata ONSENs with conserved heat response were found and together with ONSENs from other Brassicaceae were used to reconstruct the evolution of ONSEN HREs. This indicated ancestral situation with two, in palindrome organized, HSF binding motifs. In the genera Arabidopsis and Ballantinia, a local duplication of this locus increased number of HSF binding motifs to four, forming a high-efficiency HRE. In addition, whole transcriptome analysis revealed novel heat-responsive TE families COPIA20, COPIA37 and HATE. Notably, HATE represents so far unknown COPIA family which occurs in several Brassicaceae species but is absent in A. thaliana. Putative HREs were identified within the LTRs of COPIA20, COPIA37 and HATE of A. lyrata, and could be preliminarily validated by transcriptional analysis upon heat induction in subsequent survey of Brassicaeae species. Subsequent phylogenetic analysis indicated a repeated evolution of heat responsiveness within Brassicaceae COPIA LTR-retrotransposons. This indicates that acquisition of heat responsiveness may represent a successful strategy for survival of TEs within the host genome

Chromatin dynamics during interphase and cell division:similarities and differences between model and crop plants

Genetic information in the cell nucleus controls organismal development, responses to the environment and finally ensures own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organisation of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to the genome size, ploidy and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organisation and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits

Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements

Background: The mobilization of transposable elements (TEs) is suppressed by host genome defense mechanisms. Recent studies showed that the cis-regulatory region of Arabidopsis thaliana COPIA78/ONSEN retrotransposons contains heat-responsive elements (HREs), which cause their activation during heat stress. However, it remains unknown whether this is a common and potentially conserved trait and how it has evolved. Results: We show that ONSEN, COPIA37, TERESTRA, and ROMANIAT5 are the major families of heat-responsive TEs in A. lyrata and A. thaliana. Heat-responsiveness of COPIA families is correlated with the presence of putative high affinity heat shock factor binding HREs within their long terminal repeats in seven Brassicaceae species. The strong HRE of ONSEN is conserved over millions of years and has evolved by duplication of a proto-HRE sequence, which was already present early in the evolution of the Brassicaceae. However, HREs of most families are species-specific, and in Boechera stricta, the ONSEN HRE accumulated mutations and lost heat-responsiveness. Conclusions: Gain of HREs does not always provide an ultimate selective advantage for TEs, but may increase the probability of their long-term survival during the co-evolution of hosts and genomic parasites

Improving the Annotation of <i>Arabidopsis lyrata</i> Using RNA-Seq Data

<div><p>Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the <i>Arabidopsis lyrata</i> gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.</p></div

Heat stress induces alternative splicing events.

<p><b>(A)</b> Examples of differentially expressed isoforms in response to heat stress in <i>A</i>. <i>lyrata</i>. AL3G42820 expresses a second isoform that lacks the middle exon in heat-treated samples (HS). Transcripts from wild-type (WT) and recovery (REC) samples contain all three exons. AL2G15640 retains an intron in response to heat stress (HS) while wild-type (WT) and recovery (REC) samples show partial intron splicing. <b>(B)</b> Number of differential splicing events, including alternative 5’ and 3’ splice sites, mutually exclusive exons, intron retention, and exon skipping events identified with MATs based on version-1 and version-2 annotations.</p

Examples of version-1 gene models split and merged in <i>A</i>. <i>lyrata</i> gene annotation version-2.

<p><b>(A)</b> Example of a gene model that was split into two gene models in version-2. Reverse transcription-PCR could not confirm the connection of both. <b>(B)</b> Example of version-1 gene models that were merged during the annotation update. Reverse transcription-PCR confirmed presence of a transcript bridging the two version-1 genes.</p

Updating the gene model annotation of <i>A</i>. <i>lyrata</i>.

<p><b>(A)</b> Left, version-2 gene models predicted by Augustus [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137391#pone.0137391.ref028" target="_blank">28</a>]. Number of gene models overlapping with version-1 (yellow), genes predicted with Cufflinks (red), and genes with expression evidence (blue). Right, gene models of the version-1 annotation. Number of models without overlap to version-2 models (yellow), without orthologs in five other Brassicaceae (red), and without significant expression evidence (blue). <b>(B)</b> Correlation of the lengths of <i>A</i>. <i>lyrata</i> gene models with the length of their orthologous gene models in <i>A</i>. <i>thaliana</i>. Left, <i>A</i>. <i>lyrata</i> version-1 gene models. Correlations using version-1 gene models (left), version-2 gene models before (middle) and after (right) the homology-based correction of gene models. <b>(C)</b> Length distribution of gene models including genes that were removed or newly added in the version-2.</p