A Tutorial of EDTA: Extensive De Novo TE Annotator

Su, Weijia; Ou, Shujun; Hufford, Matthew B.; Peterson, Thomas

doi:10.1007/978-1-0716-1134-0_4

Cited by 32 publications

(19 citation statements)

References 17 publications

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“…Despite the increase in the number of sequenced plant genomes, manual identification remains labor-intensive, and automated TE annotation is needed [ 60 ]. Intact TEs are the complete structures of TEs that can transpose throughout the genome [ 82 ]. Most sequenced plant genomes have had annotated TEs.…”

Section: Resultsmentioning

confidence: 99%

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

et al. 2021

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Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

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Section: Resultsmentioning

confidence: 99%

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

et al. 2021

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“…This may be a result of previous studies not utilizing a dedicated LTR detection step in their repeat annotation pipeline, which is now recommended or standard practice for several popular repeat annotation programs including RepeatModeler 2 [32] and EDTA. The depauperate number of long and short interspersed nuclear elements (LINE/SINE) in our repeat annotations of prior assemblies compared to previous estimates may be a product of this difference as LINE and SINE elements can be nested within larger LTR elements [33].…”

Section: Transposable Element Content and Evolutionmentioning

confidence: 60%

De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

Linscott

González-González

Hirano

et al. 2022

Preprint

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Background Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. Results Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2–3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome. Conclusions Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs

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“…We displayed all aligned fragments with length ≥ 100 bp and identity ≥ 80% in Circos plots and highlighted alignments with identity ≥ 95% to characterize the distribution and number of plastome transferred fragments on nuclear chromosomes in different assembly versions. EDTA v1.9.4 [ 41 ] was used to annotate the repeated sequences of the nuclear genome and the TE content in the corresponding size intervals mentioned above.…”

Section: Methodsmentioning

confidence: 99%

Evaluation of Intracellular Gene Transfers from Plastome to Nuclear Genome across Progressively Improved Assemblies for Arabidopsis thaliana and Oryza sativa

Wang

Liao

Tembrock

et al. 2022

Genes

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DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species.

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A Tutorial of EDTA: Extensive De Novo TE Annotator

Cited by 32 publications

References 17 publications

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

Evaluation of Intracellular Gene Transfers from Plastome to Nuclear Genome across Progressively Improved Assemblies for Arabidopsis thaliana and Oryza sativa

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