The Genome of the “Sea Vomit” <i>Didemnum vexillum</i>
Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative s...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-12-01
|
| Series: | Life |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-1729/11/12/1377 |
| _version_ | 1797502952857927680 |
|---|---|
| author | Ernesto Parra-Rincón Cristian A. Velandia-Huerto Adriaan Gittenberger Jörg Fallmann Thomas Gatter Federico D. Brown Peter F. Stadler Clara I. Bermúdez-Santana |
| author_facet | Ernesto Parra-Rincón Cristian A. Velandia-Huerto Adriaan Gittenberger Jörg Fallmann Thomas Gatter Federico D. Brown Peter F. Stadler Clara I. Bermúdez-Santana |
| author_sort | Ernesto Parra-Rincón |
| collection | DOAJ |
| description | Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt <i>Didemnum vexillum</i>, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the <i>D. vexillum</i> genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians. |
| first_indexed | 2024-03-10T03:43:32Z |
| format | Article |
| id | doaj.art-fd7dcbd248ac44eea1e8cb5758d11d70 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:43:32Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-fd7dcbd248ac44eea1e8cb5758d11d702023-11-23T09:14:35ZengMDPI AGLife2075-17292021-12-011112137710.3390/life11121377The Genome of the “Sea Vomit” <i>Didemnum vexillum</i>Ernesto Parra-Rincón0Cristian A. Velandia-Huerto1Adriaan Gittenberger2Jörg Fallmann3Thomas Gatter4Federico D. Brown5Peter F. Stadler6Clara I. Bermúdez-Santana7Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, ColombiaBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, GermanyGiMaRIS, Rijksstraatweg 75, 2171 AK Sassenheim, The NetherlandsBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, GermanyBioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, 04107 Leipzig, GermanyDepartamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo 05508-090, BrazilBiology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, ColombiaBiology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C 111321, ColombiaTunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt <i>Didemnum vexillum</i>, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the <i>D. vexillum</i> genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.https://www.mdpi.com/2075-1729/11/12/1377Tunicata<i>Didemnum vexillum</i>microRNAsgenome annotation |
| spellingShingle | Ernesto Parra-Rincón Cristian A. Velandia-Huerto Adriaan Gittenberger Jörg Fallmann Thomas Gatter Federico D. Brown Peter F. Stadler Clara I. Bermúdez-Santana The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> Life Tunicata <i>Didemnum vexillum</i> microRNAs genome annotation |
| title | The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> |
| title_full | The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> |
| title_fullStr | The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> |
| title_full_unstemmed | The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> |
| title_short | The Genome of the “Sea Vomit” <i>Didemnum vexillum</i> |
| title_sort | genome of the sea vomit i didemnum vexillum i |
| topic | Tunicata <i>Didemnum vexillum</i> microRNAs genome annotation |
| url | https://www.mdpi.com/2075-1729/11/12/1377 |
| work_keys_str_mv | AT ernestoparrarincon thegenomeoftheseavomitididemnumvexillumi AT cristianavelandiahuerto thegenomeoftheseavomitididemnumvexillumi AT adriaangittenberger thegenomeoftheseavomitididemnumvexillumi AT jorgfallmann thegenomeoftheseavomitididemnumvexillumi AT thomasgatter thegenomeoftheseavomitididemnumvexillumi AT federicodbrown thegenomeoftheseavomitididemnumvexillumi AT peterfstadler thegenomeoftheseavomitididemnumvexillumi AT claraibermudezsantana thegenomeoftheseavomitididemnumvexillumi AT ernestoparrarincon genomeoftheseavomitididemnumvexillumi AT cristianavelandiahuerto genomeoftheseavomitididemnumvexillumi AT adriaangittenberger genomeoftheseavomitididemnumvexillumi AT jorgfallmann genomeoftheseavomitididemnumvexillumi AT thomasgatter genomeoftheseavomitididemnumvexillumi AT federicodbrown genomeoftheseavomitididemnumvexillumi AT peterfstadler genomeoftheseavomitididemnumvexillumi AT claraibermudezsantana genomeoftheseavomitididemnumvexillumi |