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Repeat annotation of Linum tenue

dataset
posted on 2024-05-13, 08:31 authored by Marco FracassettiMarco Fracassetti, Tanja SlotteTanja Slotte, Björn NystedtBjörn Nystedt, Juanita Gutierrez-Valencia, Emma L. Berdan, Ignas Bunikis, Lucile Soler, Jacques Dainat, Verena E. Kutschera, Aleksandra Losvik, Aurelie Desamore, P. William HughesP. William Hughes, Alireza ForoozaniAlireza Foroozani, Benjamin LaenenBenjamin Laenen, Edouard Pesquet, Mohamed Abdelaziz, Olga Vinnere Pettersson, Adrian C. Brennan, Juan Arroyo
The file contains the annotation for the repetitive regions in Linum tenue.

The detection of repeats has been done with RepeatMasker/RepeatModeler (https://www.repeatmasker.org/) using a custom repeat library.

The genome has been deposited to ENA with the accession id: GCA_946122785 (Project PRJEB52918). See link below.

It is part of this article Gutiérrez-Valencia, J., Fracassetti, M., Berdan, E. L., Bunikis, I., Soler, L., Dainat, J., ... & Slotte, T. (2022). Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level. Current Biology, 32(20), 4360-4371. 10.1016/j.cub.2022.08.042


Example of the data:

1306 15.6 6.2 0.0 HSU08988 6563 6781 (22462) C MER7A DNA/MER2_type (0) 336 103


1306 = Smith-Waterman score of the match, usually complexity adjusted. The SW scores are not always directly comparable. Sometimes the complexity adjustment has been turned off, and a variety of scoring-matrices are used.

15.6 = % substitutions in matching region compared to the consensus

6.2 = % of bases opposite a gap in the query sequence (deleted bp)

0.0 = % of bases opposite a gap in the repeat consensus (inserted bp)

HSU08988 = name of query sequence

6563 = starting position of match in query sequence

7714 = ending position of match in query sequence

(22462) = no. of bases in query sequence past the ending position of match

C = match is with the Complement of the consensus sequence in the database


Funding

Supergene evolution in a classic plant system - bringing the study of distyly into the genomic era

European Research Council

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The role of structural variation for the origin and evolution of a classic supergene

Swedish Research Council

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History

Publisher

Stockholm University

SciLifeLab acknowledgement

  • Bioinformatics platform (NBIS)
  • National Genomics Infrastructure unit

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    Tanja Slotte research group

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