{"entity": "researcher", "timestamp": "2026-06-15T17:12:35.130Z", "family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-5492-1062", "affiliations": ["Institut National de la Recherche Agronomique, UPR 1258, Centre National des Ressources G\u00e9nomiques V\u00e9g\u00e9tales, 31326, Castanet-Tolosan, France."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c"}}, "publications": [{"entity": "publication", "iuid": "32a294f52192486aabddd5b6dcb69cc8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32a294f52192486aabddd5b6dcb69cc8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32a294f52192486aabddd5b6dcb69cc8"}}, "title": "A MITE insertion abolishes the AP3-3 self-maintenance regulatory loop in apetalous flowers of Nigella damascena.", "authors": [{"family": "Conde E Silva", "given": "Natalia", "initials": "N", "orcid": "0000-0003-2435-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/bdec1fbe4d50482198c6759f4c47e462.json"}}, {"family": "Leguilloux", "given": "Martine", "initials": "M"}, {"family": "Bellec", "given": "Arnaud", "initials": "A", "orcid": "0000-0002-7608-9537", "researcher": {"href": "https://publications.scilifelab.se/researcher/a9c2cdea0dd645209766bf96deb930a5.json"}}, {"family": "Rodde", "given": "Nathalie", "initials": "N", "orcid": "0000-0003-3361-4730", "researcher": {"href": "https://publications.scilifelab.se/researcher/950d614a328b44fbb3d7ac18b1b1e2ae.json"}}, {"family": "Aubert", "given": "Juliette", "initials": "J", "orcid": "0000-0001-6136-3815", "researcher": {"href": "https://publications.scilifelab.se/researcher/a60f9a06e785408e9db43e2a55b533de.json"}}, {"family": "Manicacci", "given": "Domenica", "initials": "D", "orcid": "0000-0002-6779-113X", "researcher": {"href": "https://publications.scilifelab.se/researcher/37f4aa92f5dc43d28a6795113ed48ad4.json"}}, {"family": "Damerval", "given": "Catherine", "initials": "C", "orcid": "0000-0002-7317-4971", "researcher": {"href": "https://publications.scilifelab.se/researcher/a48c5646210742ff92a211d82e35c0d7.json"}}, {"family": "Berges", "given": "Helene", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "Deveaux", "given": "Yves", "initials": "Y", "orcid": "0000-0002-3297-1317", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ef27480c1c94cc9a5d742d0dd3c1d12.json"}}], "type": "journal article", "published": "2023-03-13", "journal": {"title": "J. Exp. Bot.", "issn": "1460-2431", "volume": "74", "issue": "5", "pages": "1448-1459", "issn-l": "0022-0957"}, "abstract": "MADS-box transcription factors are important regulators of floral organ identity through their binding to specific motifs, termed CArG, in the promoter of their target genes. Petal initiation and development depend on class A and B genes, but MADS-box genes of the APETALA3 (AP3) clade are key regulators of this process. In the early diverging eudicot Nigella damascena, an apetalous [T] morph is characterized by the lack of expression of the NdAP3-3 gene, with its expression being petal-specific in the wild-type [P] morph. All [T] morph plants are homozygous for an NdAP3-3 allele with a Miniature Inverted-repeat Transposable Element (MITE) insertion in the second intron of the gene. Here, we investigated to which extent the MITE insertion impairs regulation of the NdAP3-3 gene. We found that expression of NdAP3-3 is initiated in the [T] morph, but the MITE insertion prevents its positive self-maintenance by affecting the correct splicing of the mRNA. We also found specific CArG features in the promoter of the NdAP3-3 genes with petal-specific expression. However, they are not sufficient to drive expression only in petals of transgenic Arabidopsis, highlighting the existence of Nigella-specific cis/trans-acting factors in regulating AP3 paralogs.", "doi": "10.1093/jxb/erac489", "pmid": "36512646", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "NGI Long read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pii", "key": "6895535"}], "notes": [], "created": "2023-08-15T07:02:42.318Z", "modified": "2023-08-15T07:02:42.621Z"}, {"entity": "publication", "iuid": "b8925ebd7a3d4937888410541e0f333a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8925ebd7a3d4937888410541e0f333a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8925ebd7a3d4937888410541e0f333a"}}, "title": "A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis.", "authors": [{"family": "Costa", "given": "Zirlane Portugal", "initials": "ZP", "orcid": "0000-0002-2374-0656", "researcher": {"href": "https://publications.scilifelab.se/researcher/09be41cb5cc74f08994a09c8cc550bdb.json"}}, {"family": "Varani", "given": "Alessandro Mello", "initials": "AM", "orcid": "0000-0002-8876-3269", "researcher": {"href": "https://publications.scilifelab.se/researcher/bac0ae5233a443ac9eee827b6b875109.json"}}, {"family": "Cauz-Santos", "given": "Luiz Augusto", "initials": "LA", "orcid": "0000-0003-1694-2433", "researcher": {"href": "https://publications.scilifelab.se/researcher/00517fb9a63343efaff34400c8e337b9.json"}}, {"family": "Sader", "given": "Mariela Anal\u00eda", "initials": "MA", "orcid": "0000-0001-8188-2217", "researcher": {"href": "https://publications.scilifelab.se/researcher/f223c4b873d1422e97f09e208d4f833e.json"}}, {"family": "Giopatto", "given": "Helena Augusto", "initials": "HA", "orcid": "0000-0002-4712-468X", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e989dda75f4455384ea659f6fad4822.json"}}, {"family": "Zirpoli", "given": "Bruna", "initials": "B", "orcid": "0000-0002-9477-2516", "researcher": {"href": "https://publications.scilifelab.se/researcher/50cd30fde0e5440eac28e0414aa06932.json"}}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Cauet", "given": "Stephane", "initials": "S", "orcid": "0000-0003-4985-8940", "researcher": {"href": "https://publications.scilifelab.se/researcher/09dd5de29b3244c4be6ac0c5b176a891.json"}}, {"family": "Marande", "given": "Willian", "initials": "W"}, {"family": "Souza Cardoso", "given": "Jessica Luana", "initials": "JL", "orcid": "0000-0002-0483-9060", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b4c2489aeb44d43acbe31c4f6fa3857.json"}}, {"family": "Pinheiro", "given": "Daniel Guariz", "initials": "DG", "orcid": "0000-0001-7062-5936", "researcher": {"href": "https://publications.scilifelab.se/researcher/8ef132ec65864133a921d7e5f69027cd.json"}}, {"family": "Kitajima", "given": "Jo\u00e3o Paulo", "initials": "JP"}, {"family": "Dornelas", "given": "Marcelo Carnier", "initials": "MC", "orcid": "0000-0002-6710-3050", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c1e41a1347346e8b2060ec2e8d205bb.json"}}, {"family": "Harand", "given": "Andrea Pedrosa", "initials": "AP", "orcid": "0000-0001-5213-4770", "researcher": {"href": "https://publications.scilifelab.se/researcher/a47c26fbc200429f8ff672fe28e21a30.json"}}, {"family": "Berges", "given": "Helene", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "Monteiro-Vitorello", "given": "Claudia Barros", "initials": "CB", "orcid": "0000-0002-1238-9354", "researcher": {"href": "https://publications.scilifelab.se/researcher/c507f01cbafd4175860767c82064ca37.json"}}, {"family": "Carneiro Vieira", "given": "Maria Lucia", "initials": "ML", "orcid": "0000-0003-0341-5714", "researcher": {"href": "https://publications.scilifelab.se/researcher/8eb37815cd9e4577b677fd053bf6e15c.json"}}], "type": "journal article", "published": "2021-07-23", "journal": {"title": "Plant Genome", "issn": "1940-3372", "pages": "e20117", "issn-l": "1940-3372"}, "abstract": "The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (\u223c500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining self-incompatibility and the MADS-box gene family, allowing us to infer expansions and contractions within specific subfamilies. Finally, we recovered the organellar DNA. Structural rearrangements and two mitoviruses, besides relics of other mobile elements, were found in the chloroplast and mt-DNA molecules, respectively. This study presents the first draft genome assembly of a wild Passiflora species, providing a valuable sequence resource for genomic and evolutionary studies on the genus, and support for breeding cropped passionfruit species.", "doi": "10.1002/tpg2.20117", "pmid": "34296827", "labels": {"NGI Uppsala (Uppsala Genome Center)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2021-08-05T12:08:47.355Z", "modified": "2021-11-10T12:23:17.044Z"}, {"entity": "publication", "iuid": "e0e653f6b4f54d8584da0f7e3225d6ab", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e0e653f6b4f54d8584da0f7e3225d6ab"}}, "title": "Genetic basis and timing of a major mating system shift in Capsella.", "authors": [{"family": "Bachmann", "given": "J\u00f6rg A", "initials": "JA"}, {"family": "Tedder", "given": "Andrew", "initials": "A", "orcid": "0000-0002-7378-4673", "researcher": {"href": "https://publications.scilifelab.se/researcher/8a29b3c1160f46bf8b21e331268eb4b1.json"}}, {"family": "Laenen", "given": "Benjamin", "initials": "B"}, {"family": "Fracassetti", "given": "Marco", "initials": "M", "orcid": "0000-0002-2962-2669", "researcher": {"href": "https://publications.scilifelab.se/researcher/695213cdd1a645cbbf10d44122237b18.json"}}, {"family": "D\u00e9samor\u00e9", "given": "Aur\u00e9lie", "initials": "A", "orcid": "0000-0003-1922-3557", "researcher": {"href": "https://publications.scilifelab.se/researcher/e117d822871c4a38960b526e3d0dcd0a.json"}}, {"family": "Lafon-Placette", "given": "Cl\u00e9ment", "initials": "C", "orcid": "0000-0001-6634-8104", "researcher": {"href": "https://publications.scilifelab.se/researcher/63262f71f9c54f438d6f08380d799d96.json"}}, {"family": "Steige", "given": "Kim A", "initials": "KA"}, {"family": "Callot", "given": "Caroline", "initials": "C"}, {"family": "Marande", "given": "William", "initials": "W"}, {"family": "Neuffer", "given": "Barbara", "initials": "B"}, {"family": "Berg\u00e8s", "given": "H\u00e9l\u00e8ne", "initials": "H", "orcid": "0000-0002-5492-1062", "researcher": {"href": "https://publications.scilifelab.se/researcher/728be2338bd2407980d11b8850d85d9c.json"}}, {"family": "K\u00f6hler", "given": "Claudia", "initials": "C", "orcid": "0000-0002-2619-4857", "researcher": {"href": "https://publications.scilifelab.se/researcher/accd3f9307614c8ab67154dd5e50cdac.json"}}, {"family": "Castric", "given": "Vincent", "initials": "V", "orcid": "0000-0002-4461-4915", "researcher": {"href": "https://publications.scilifelab.se/researcher/f891128567d64aaba03bdd9f4bc5d458.json"}}, {"family": "Slotte", "given": "Tanja", "initials": "T", "orcid": "0000-0001-6020-5102", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c69ee78bae41478465a7e5fa63b946.json"}}], "type": "journal article", "published": "2019-10-00", "journal": {"volume": "224", "issn": "1469-8137", "issue": "1", "pages": "505-517", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male specificity components, encoded by the genes SRK and SCR at the self-incompatibility locus (S-locus). Theory predicts that S-linked mutations, and especially dominant mutations in SCR, are likely to contribute to loss of SI. However, few studies have investigated the contribution of dominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer species Capsella orientalis, by combining genetic mapping, long-read sequencing of complete S-haplotypes, gene expression analyses and controlled crosses. We show that loss of SI in C. orientalis occurred < 2.6 Mya and maps as a dominant trait to the S-locus. We identify a fixed frameshift deletion in the male specificity gene SCR and confirm loss of male SI specificity. We further identify an S-linked small RNA that is predicted to cause dominance of self-compatibility. Our results agree with predictions on the contribution of dominant S-linked mutations to loss of SI, and thus provide new insights into the molecular basis of mating system transitions.", "doi": "10.1111/nph.16035", "pmid": "31254395", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "GENBANK", "key": "PRJEB32122"}, {"db": "GENBANK", "key": "KJ772374.1"}], "notes": [], "created": "2019-12-03T10:47:11.816Z", "modified": "2024-01-16T13:48:43.769Z"}]}