scholarly journals Plant Genome Analysis in France: From the Functional Analysis of the Arabidopsis Thaliana Genome to GENOPLANTE

10.1038/70378 ◽  
1999 ◽  
Vol 17 (S5) ◽  
pp. 24-24
Author(s):  
Michel Caboche
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana ◽  
Genome Analysis ◽  
Plant Genome ◽  
Arabidopsis Thaliana Genome

scholarly journals Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2681
Author(s):  
Ilya Kirov ◽  
Pavel Merkulov ◽  
Maxim Dudnikov ◽  
Ekaterina Polkhovskaya ◽  
Roman A. Komakhin ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Assembly ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Gag Protein ◽  
Reading Frame ◽  
Retrotransposon Family ◽  
Long Read ◽  
Low Coverage ◽  
Arabidopsis Thaliana Genome

Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.

scholarly journals Functional Analysis of the Arabidopsis thaliana CDPK-Related Kinase Family: AtCRK1 Regulates Responses to Continuous Light

2018 ◽  
Vol 19 (5) ◽  
pp. 1282 ◽  
Author(s):  
Abu Baba ◽  
Gábor Rigó ◽  
Ferhan Ayaydin ◽  
Ateeq Rehman ◽  
Norbert Andrási ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana ◽  
Continuous Light ◽  
Kinase Family

Functional Analysis of Two PsbP-Like (PPL) Proteins in Arabidopsis thaliana

2008 ◽  
pp. 1085-1088 ◽  
Author(s):  
Seiko Ishihara ◽  
Atsushi Takabayashi ◽  
Tsuyoshi Endo ◽  
Kentaro Ifuku ◽  
Fumihiko Sato
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana

Molecular cloning and functional analysis of lotus salt-induced NnDREB2C, NnPIP1-2 and NnPIP2-1 in Arabidopsis thaliana

2019 ◽  
Vol 47 (1) ◽  
pp. 497-506 ◽  
Author(s):  
Liu Ziyuan ◽  
Wang Chunfei ◽  
Yang Jianjun ◽  
Liu Xian ◽  
Li Liangjun ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Arabidopsis Thaliana ◽  
Molecular Cloning
Sign in / Sign up

Export Citation Format

Share Document