ArticleThe Plant journal : for cell and molecular biology2021
Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research.
Article in The Plant journal : for cell and molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 35 citations in OpenAlex.
- Evolutionary dynamics of the proanthocyanidin biosynthesis gene LAR.BMC genomics · 2025Article
- Phytochrome A is required for light-inhibited germination of Aethionema arabicum seed.The New phytologist · 2025Article
- Emergence of isochorismate-based salicylic acid biosynthesis within Brassicales.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication.G3 (Bethesda, Md.) · 2025Article
- Multiomic analysis reveals that the flavonoid biosynthesis pathway is associated with cold tolerance inFrontiers in plant science · 2025Article
- Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana.G3 (Bethesda, Md.) · 2024Article
- The dimorphic diaspore model Aethionema arabicum (Brassicaceae): Distinct molecular and morphological control of responses to parental and germination temperatures.The Plant cell · 2024Article
- Article
- Approaches to increase the validity of gene family identification using manual homology search tools.Genetica · 2023Review
- Evolutionary Dynamics ofPlants (Basel, Switzerland) · 2023Article
- Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum.Plant physiology · 2023Article
- Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo.International journal of molecular sciences · 2023Review
- Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.Genome biology and evolution · 2023Article
- PEATmoss: A Gene Expression Atlas for Bryophytes.Methods in molecular biology (Clifton, N.J.) · 2023Article
- EasyGDB: a low-maintenance and highly customizable system to develop genomics portals.Bioinformatics (Oxford, England) · 2022Article
- Comparative transcriptomics identifies candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae).BMC plant biology · 2022Article
- Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species.Applications in plant sciencesArticle
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Authors and funding
11 authors at 6 institutions in 5 countries.
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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 Iso-seq 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-α 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-β 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).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.