Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. / Fernandez-Pozo, Noe; Metz, Timo; Chandler, Jake; Gramzow, Lydia; Merai, Zsuzsanna; Maumus, Florian; Mittelsten Scheid, Ortrun; Theißen, Günter; Schranz, Michael Eric; Leubner-Metzger, Gerhard; Rensing, Stefan.

In: Plant Journal, 16.01.2021.

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Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. / Fernandez-Pozo, Noe; Metz, Timo; Chandler, Jake; Gramzow, Lydia; Merai, Zsuzsanna; Maumus, Florian; Mittelsten Scheid, Ortrun; Theißen, Günter; Schranz, Michael Eric; Leubner-Metzger, Gerhard; Rensing, Stefan.

In: Plant Journal, 16.01.2021.

Research output: Contribution to journalArticlepeer-review

Harvard

APA

Fernandez-Pozo, N., Metz, T., Chandler, J., Gramzow, L., Merai, Z., Maumus, F., Mittelsten Scheid, O., Theißen, G., Schranz, M. E., Leubner-Metzger, G., & Rensing, S. (2021). Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. Plant Journal. https://doi.org/10.1111/tpj.15161

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Author

Fernandez-Pozo, Noe ; Metz, Timo ; Chandler, Jake ; Gramzow, Lydia ; Merai, Zsuzsanna ; Maumus, Florian ; Mittelsten Scheid, Ortrun ; Theißen, Günter ; Schranz, Michael Eric ; Leubner-Metzger, Gerhard ; Rensing, Stefan. / Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. In: Plant Journal. 2021.

BibTeX

@article{6108158fcda045a483b6aa32a6350203,
title = "Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research",
abstract = "Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Isoseq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-a polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-b and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).",
author = "Noe Fernandez-Pozo and Timo Metz and Jake Chandler and Lydia Gramzow and Zsuzsanna Merai and Florian Maumus and {Mittelsten Scheid}, Ortrun and G{\"u}nter Thei{\ss}en and Schranz, {Michael Eric} and Gerhard Leubner-Metzger and Stefan Rensing",
year = "2021",
month = jan,
day = "16",
doi = "10.1111/tpj.15161",
language = "English",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",

}

RIS

TY - JOUR

T1 - Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

AU - Fernandez-Pozo, Noe

AU - Metz, Timo

AU - Chandler, Jake

AU - Gramzow, Lydia

AU - Merai, Zsuzsanna

AU - Maumus, Florian

AU - Mittelsten Scheid, Ortrun

AU - Theißen, Günter

AU - Schranz, Michael Eric

AU - Leubner-Metzger, Gerhard

AU - Rensing, Stefan

PY - 2021/1/16

Y1 - 2021/1/16

N2 - Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Isoseq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-a polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-b and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).

AB - Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Isoseq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-a polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-b and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).

U2 - 10.1111/tpj.15161

DO - 10.1111/tpj.15161

M3 - Article

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

ER -