A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis
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 (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosyste...
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2021
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oai:doaj.org-article:e4ec74a6041e43a784346c6a8aaa1c202021-12-05T07:50:12ZA genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis1940-337210.1002/tpg2.20117https://doaj.org/article/e4ec74a6041e43a784346c6a8aaa1c202021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20117https://doaj.org/toc/1940-3372Abstract The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) 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.Zirlane Portugal CostaAlessandro Mello VaraniLuiz Augusto Cauz‐SantosMariela Analía SaderHelena Augusto GiopattoBruna ZirpoliCaroline CallotStephane CauetWillian MarandeJessica Luana Souza CardosoDaniel Guariz PinheiroJoão Paulo KitajimaMarcelo Carnier DornelasAndrea Pedrosa HarandHelene BergesClaudia Barros Monteiro‐VitorelloMaria Lucia Carneiro VieiraWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021) |
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Plant culture SB1-1110 Genetics QH426-470 |
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Plant culture SB1-1110 Genetics QH426-470 Zirlane Portugal Costa Alessandro Mello Varani Luiz Augusto Cauz‐Santos Mariela Analía Sader Helena Augusto Giopatto Bruna Zirpoli Caroline Callot Stephane Cauet Willian Marande Jessica Luana Souza Cardoso Daniel Guariz Pinheiro João Paulo Kitajima Marcelo Carnier Dornelas Andrea Pedrosa Harand Helene Berges Claudia Barros Monteiro‐Vitorello Maria Lucia Carneiro Vieira A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| description |
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 (∼500) 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. |
| format |
article |
| author |
Zirlane Portugal Costa Alessandro Mello Varani Luiz Augusto Cauz‐Santos Mariela Analía Sader Helena Augusto Giopatto Bruna Zirpoli Caroline Callot Stephane Cauet Willian Marande Jessica Luana Souza Cardoso Daniel Guariz Pinheiro João Paulo Kitajima Marcelo Carnier Dornelas Andrea Pedrosa Harand Helene Berges Claudia Barros Monteiro‐Vitorello Maria Lucia Carneiro Vieira |
| author_facet |
Zirlane Portugal Costa Alessandro Mello Varani Luiz Augusto Cauz‐Santos Mariela Analía Sader Helena Augusto Giopatto Bruna Zirpoli Caroline Callot Stephane Cauet Willian Marande Jessica Luana Souza Cardoso Daniel Guariz Pinheiro João Paulo Kitajima Marcelo Carnier Dornelas Andrea Pedrosa Harand Helene Berges Claudia Barros Monteiro‐Vitorello Maria Lucia Carneiro Vieira |
| author_sort |
Zirlane Portugal Costa |
| title |
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| title_short |
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| title_full |
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| title_fullStr |
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| title_full_unstemmed |
A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis |
| title_sort |
genome sequence resource for the genus passiflora, the genome of the wild diploid species passiflora organensis |
| publisher |
Wiley |
| publishDate |
2021 |
| url |
https://doaj.org/article/e4ec74a6041e43a784346c6a8aaa1c20 |
| work_keys_str_mv |
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