TY  - JOUR
AB  - BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.
AU  - Peona, V.*
AU  - Martelossi, J.*
AU  - Almojil, D.*
AU  - Bocharkina, J.*
AU  - Brännström, I.*
AU  - Brown, M.*
AU  - Cang, A.*
AU  - Carrasco-Valenzuela, T.*
AU  - deVries, J.H.*
AU  - Doellman, M.*
AU  - Elsner, D.*
AU  - Espíndola-Hernández, P.
AU  - Montoya, G.F.*
AU  - Gaspar, B.*
AU  - Zagorski, D.*
AU  - Hałakuc, P.*
AU  - Ivanovska, B.*
AU  - Laumer, C.*
AU  - Lehmann, R.*
AU  - Boštjančić, L.L.*
AU  - Mashoodh, R.*
AU  - Mazzoleni, S.*
AU  - Mouton, A.*
AU  - Nilsson, M.A.*
AU  - Pei, Y.*
AU  - Potente, G.*
AU  - Provataris, P.*
AU  - Pardos-Blas, J.R.*
AU  - Raut, R.*
AU  - Sbaffi, T.*
AU  - Schwarz, F.*
AU  - Stapley, J.*
AU  - Stevens, L.*
AU  - Sultana, N.*
AU  - Symonova, R.*
AU  - Tahami, M.S.*
AU  - Urzì, A.*
AU  - Yang, H.*
AU  - Yusuf, A.*
AU  - Pecoraro, C.*
AU  - Suh, A.*
C1  - 70620
C2  - 56103
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.
JO  - Mob. DNA
VL  - 15
IS  - 1
PB  - Bmc
PY  - 2024
SN  - 1759-8753
ER  - 

TY  - JOUR
AB  - Background: While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. Results: Here, we present an analysis of the repetitive fraction of the 5100 Mb barley genome, the largest angiosperm genome to have a near-complete sequence assembly. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low copy numbers. We found that the barley genome is highly compartmentalized with different types of TEs occupying different chromosomal "niches", such as distal, interstitial, or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Furthermore, their presence in gene promoters is associated with decreased methylation levels. Conclusions: Our data show that TEs are major determinants of overall chromosome structure. We hypothesize that many of the the various chromosomal distribution patterns are the result of TE families targeting specific niches, rather than them accumulating where they have the least deleterious effects.
AU  - Wicker, T.*
AU  - Schulman, A.H.*
AU  - Tanskanen, J.*
AU  - Spannagl, M.
AU  - Twardziok, S.O.
AU  - Mascher, M.*
AU  - Springer, N.M.*
AU  - Li, Q.*
AU  - Waugh, R.*
AU  - Li, C.*
AU  - Zhang, G.*
AU  - Stein, N.*
AU  - Mayer, K.F.X.*
AU  - Gundlach, H.
C1  - 52591
C2  - 44106
CY  - London
TI  - The repetitive landscape of the 5100 Mbp barley genome.
JO  - Mob. DNA
VL  - 8
IS  - 1
PB  - Biomed Central Ltd
PY  - 2017
SN  - 1759-8753
ER  -