A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

Abstract Background Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strai...

Full description

Bibliographic Details
Published in:	BMC Genomics
Main Authors:	Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint-Jean, Grégory Carrier
Format:	Article
Language:	English
Published:	BMC 2018-05-01
Subjects:	Transposable elements Genome assembly Pipeline Tool Annotation Algae
Online Access:	http://link.springer.com/article/10.1186/s12864-018-4763-1

Similar Items

Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits.
by: Jérémy Berthelier, et al.
Published: (2023-01-01)

Phenotype stability and dynamics of transposable elements in a strain of the microalga Tisochrysis lutea with improved lipid traits
by: Jérémy Berthelier, et al.
Published: (2023-01-01)

The good, the bad and the ugly of transposable elements annotation tools
by: Elgion L. S. Loreto, et al.
Published: (2024-02-01)

Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation
by: Xuanzeng Liu, et al.
Published: (2024-03-01)

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
by: The TE Hub Consortium, et al.
Published: (2021-06-01)

Characterization of transposable elements within the Bemisia tabaci species complex
by: Juan Paolo A. Sicat, et al.
Published: (2022-04-01)

Efficient homology‐based annotation of transposable elements using minimizers
by: Laura Natalia Gonzalez‐García, et al.
Published: (2023-07-01)

RepetDB: a unified resource for transposable element references
by: Joëlle Amselem, et al.
Published: (2019-01-01)

The chloroplast genome of the marine microalga Tisochrysis lutea
by: Alejandra B. Méndez-Leyva, et al.
Published: (2019-01-01)

Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
by: José A. Valdes Franco, et al.
Published: (2018-04-01)

Identification and frequency of transposable elements in Eucalyptus
by: Maurício Bacci Jr., et al.
Published: (2005-01-01)

Identification of cell-type-specific, transcriptionally active transposable elements using long-read RNA-sequencing data-based comprehensive annotation
by: Chaemin Lim, et al.
Published: (2025-08-01)

Monitoring Changes to Alkenone Biosynthesis in Commercial Tisochrysis lutea Microalgae
by: Gregory W. O’Neil, et al.
Published: (2024-03-01)

Toxicity of herbicides to the marine microalgae Tisochrysis lutea and Tetraselmis sp.
by: Florita Flores, et al.
Published: (2024-01-01)

Identification of transposable element families from pangenome polymorphisms
by: Pío Sierra, et al.
Published: (2024-06-01)

Transposable elements as essential elements in the control of gene expression
by: Alemu Gebrie
Published: (2023-08-01)

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data
by: Michael G. Nelson, et al.
Published: (2017-08-01)

Characterization of active transposable elements and their new insertions in tuber propagated greater yam (Dioscorea alata)
by: Sajjad Ali Panhwar, et al.
Published: (2024-09-01)

Accelerating de novo SINE annotation in plant and animal genomes
by: Herui Liao, et al.
Published: (2024-10-01)

Analysis of Transposable Elements in Coccidioides Species
by: Theo N. Kirkland, et al.
Published: (2018-01-01)

Transposable elements as key regulators of placental development
by: M. A. Zhilkina, et al.
Published: (2025-09-01)

Transposable elements from the mesophragmatica group of Drosophila
by: Erika Germanos, et al.
Published: (2006-01-01)

Cell Cycle Dynamics in the Microalga <i>Tisochrysis lutea</i>: Influence of Light Duration and Drugs
by: Laura Pageault, et al.
Published: (2024-11-01)

Editorial: The epigenetic control of transposable elements in development and in diseases
by: Jan Padeken, et al.
Published: (2023-09-01)

Long-read RNA sequencing enables full-length chimeric transcript annotation of transposable elements in lung adenocarcinoma
by: Yang Li, et al.
Published: (2025-03-01)

Involvement of transposable elements in neurogenesis
by: R. N. Mustafin, et al.
Published: (2020-04-01)

Transposable Element Is Predictive of Chemotherapy- and Immunotherapy-Related Overall Survival in Glioma
by: Bi Peng, et al.
Published: (2025-05-01)

All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing
by: Luisa Di Stefano
Published: (2022-08-01)

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
by: Yuh Chwen G Lee, et al.
Published: (2017-07-01)

Asexual reproduction reduces transposable element load in experimental yeast populations
by: Jens Bast, et al.
Published: (2019-09-01)

The role of transposable elements in the ecological morphogenesis under the influence of stress
by: R. N. Mustafin, et al.
Published: (2019-07-01)

Constitutive Heterochromatin in Eukaryotic Genomes: A Mine of Transposable Elements
by: René Massimiliano Marsano, et al.
Published: (2022-02-01)

Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns
by: Nunzia Colonna Romano, et al.
Published: (2022-03-01)

Diversity and evolution of transposable elements in the plant-parasitic nematodes
by: Mehmet Dayi
Published: (2024-05-01)

RepBox: a toolbox for the identification of repetitive elements
by: Shelvasha Burkes-Patton, et al.
Published: (2023-08-01)

Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences
by: Xiaoyu Yu
Published: (2023-05-01)

MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
by: Alexander Eng, et al.
Published: (2020-10-01)

International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany
by: Pascale Lesage, et al.
Published: (2016-10-01)

Bioinformatics Analysis of Evolution and Human Disease Related Transposable Element-Derived microRNAs
by: Hee-Eun Lee, et al.
Published: (2020-06-01)

Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions
by: Verneret, Marie, et al.
Published: (2025-06-01)