Symposium proposal |
Organizer: | Yong E. Zhang (Institute of Zoology, Chinese Academy of Sciences) |
Co-organizer: | Jinfeng Chen ( Institute of Zoology, Chinese Academy of Sciences) |
Ever since McClintock, decades of research has revealed transposable elements (TEs) as a major catalyst of genome evolution by mediating both regulatory and coding changes. The recent surge of short and long read sequencing techniques begins to unmask an even more complete landscape on how TEs shape variations between species, between populations, between individuals or even between cells. This symposium aims to provide an updated view on how TEs emerge, how they are regulated and, how they contribute to phenotypic variation.
Three scholars agree to join. Dr. Susan Wessler pioneers the use of genome-wide approaches in studying transposable element, and is well known for her study of plant transposable elements in gene and genome evolution. Dr. Josefa González is well known for her research in the field of environmental adaptation especially in how TEs shape adaptive evolution in Drosophila. Dr. Zhao Zhang is well known for his research on the regulation of transposons in germ cells and somatic tissue and their influence on reproduction, development, aging, and disease.
We believe that these invited speakers will bring deep insights given their work in the relevant topics. By bringing together both evolutionary geneticists and molecular geneticists, the symposium may catalyze a deeper mechanistic understanding of TEs in genetics and evolution. |
S6-1
The role of transposable elements in environmental adaptation
Josefa Gonzalez1
1Institute of Evolutionary Biology (CSIC-UPF)
How organisms adapt to the environment is still an open question in Biology. Short read genome sequencing has allowed to explore in depth the role of single nucleotide polymorphisms (SNPs) in environmental adaptation. However, SNPs alone can only explain a fraction of the existing ecologically relevant phenotypic variation. Among the structural variants that can now be studied thanks to the availability of long-read sequencing, transposable elements are likely to play a major role in adaptation due to their capacity to generate mutations that often have phenotypic effects of a complexity that is not achievable by point mutations. Drosophila melanogaster is an excellent model species to quantify the role of transposable elements in environmental adaptation as it has recently colonized very distinct environments. We have generated 32 new D. melanogaster reference genomes using long-read sequencing of natural populations collected in arid, cold and temperate environments. We have discovered thousands of new transposable element insertions including copies from three new families. We have also generated transcriptomic data for 18 of these genomes, which is allowing us to elucidate the role of transposable elements in expression quantitative trait loci (eQTL) variation. Finally, we are also investigating the role of the identified insertions in desiccation, oxidative and heavy-metal stress responses as well as in immune response. To do this, we are using a combination of RNA-seq, ChIP-seq and Hi-C, with in vivo enhancer assays and CRISPR/Cas9 editing. Overall, our results are providing evidence for a significant role of transposable elements in environmental adaptation.
S6-2
Retrotransposon renders protection against future viral infection by triggering trained immunity
Zhao Zhang1
1Duke University
Transposons are the most abundant residents in the genomes of nearly all animals. Their uncontrolled activation is linked to sterility, cancer, and other pathological conditions, thereby being largely considered detrimental. Here we report within a strictly defined time window of development, transposon activation can license the host’s immune system for future anti-viral responses. We found the Gypsy retrotransposon selectively becomes active during metamorphosis at the Drosophila pupal stage. At this stage, Gypsy activation primes the host’s innate immune system by inducing the systemic anti-viral function of the NF-kB protein, Relish. Consequently, adult flies with Gypsy or Relish silenced at the pupal stage are unable to clear exogenous viruses and succumb to viral infection. Altogether, our data reveal that programed activation of transposons during development establishes trained immunity and endows a long-term benefit in pathogen warfare.
S6-3
Deciphering the strategies evolved by a very successful transposable element
Susan R Wessler1, Jinfeng Chen1, LuLu1, Jason Stajich1, Yutaka Okumoto2,2
1University of California Riverside, USA
2Setsunan University, Osaka, Japan
Transposable elements (TEs) achieve high copy numbers through waves of amplification called bursts. For a TE to successfully burst it must be able to significantly increase its copy number without killing its host or being silenced by genome surveillance (epigenetic) mechanisms. However, because the vast majority of TE bursts have been inferred after the fact - via computational analysis of whole genome sequence- stealth features they require for success have remained largely undiscovered.
Some features have recently been discovered by analyzing active bursts of the miniature inverted repeat transposable element (MITE) mPing and its autonomous partner Ping in four accessions of domesticated rice (Oryza sativa, temperate japonica). First, mPing targets genic regions but avoids exon sequences, thus minimizing harm to the host. Second, because mPing does not share coding sequences with Ping, increases in its copy number and host recognition of its sequences do not silence Ping genes, thus allowing the continuous production of the proteins necessary to sustain the burst for decades.
Additional insights into the mPing burst comes from analyses of an extensive collection of rice genomes including 3000 domesticated strains and a recombinant inbred population. While the survey of 3000 strains revealed that the burst is very recent and is restricted to a few closely related accessions, analysis of the sequences of 272 recombinant inbred lines demonstrated the potential of mPing to rapidly spread unimpeded through a large population, increasing both the number of new insertions into gene regulatory regions and the frequency of structural variations.
S6-4
Non-model animal perspectives on the annotation of transposable elements
Alexander Suh1
1School of Biological Sciences, University of East Anglia, United Kingdom
2Department of Organismal Biology, Uppsala University, Sweden
The identification and classification of transposable elements (TEs) has become one of the key bottlenecks of comparative genomics analyses, particularly of non-model animals. Here I discuss lessons learned from previous and ongoing TE annotation projects where manual curation proved vital for classification of "unknown" repeats. Furthermore, I highlight the need for community initiatives to crowd-source manual curation efforts as well as wiki-style open databases.
S6-5
The evolution of 26 diverse maize genomes driven by transposable elements
Shujun Ou1, Sarah Anderson2, Jonathan Gent3, Arun Seetharam1, Nancy Manchanda1, Candice Hirsch4, Matthew Hufford1
1Department of Ecology, Evolution, and Organismal Biology
2Genetics, Development, and Cell Biology
3Department of Plant Biology
4Department of Agronomy and Plant Genetics
High-quality genomes have become increasingly available thanks to advances in sequencing technology. So far, there are over 30 maize genomes available, including the 26 recently released NAM founder genomes. Transposable elements (TEs) comprise over 80% of maize genomes and contribute to the extensive genetic variation found across lines. To study TE dynamics within the diverse NAM founders, we developed a pan-genome TE annotation module within EDTA (Ou et al. 2019) for consistent and accurate annotations in each genome. Our annotation revealed that approximately 31% of TEs are structurally intact, and 69% are fragmented. Annotation across all NAM genomes identified over 27,000 TE families, though the largest 500 families comprised 93% of the total TE space. We also identified 393,000 intact singleton TEs (2.2% of the TE space) that could not be classified. Comparing between NAM lines, we find that tropical maize genomes are ~54 Mb larger than temperate genomes, a difference that is mainly driven by LTR-RTs and Helitrons. This can be attributed to the combined effects of TE proliferation in tropical lines and removal in temperate lines. Further, we identified 25 active LTR-RT families contributing more new copies in tropical maize than temperate maize post domestication (< 10 ka). Finally, we explore how methylation status, accessible chromatin regions, and patterns of expression in 10 tissues may contribute to the variable activity of these families contributing to the difference in genome sizes between tropical and temperate genomes.