Re-annotation improved large-scale assembly of the reef-building coral Acropora intermedia Article Swipe
Xinyao Chang
,
Wentao Han
,
Xiaomei Chen
,
C. J. Tang
,
Danyang Wang
,
Heng Huang
,
Yuli Li
,
Kai Chen
,
Jingjie Hu
,
Zhenmin Bao
,
Hong Chen
,
Shi Wang
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1038/s41597-025-05849-1
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1038/s41597-025-05849-1
Acropora corals, primary reef-builders providing habitat for numerous marine species, now face novel survival pressures due to environmental changes. Acropora intermedia (Brook 1891), a significant contributor to the vibrant ecosystems of coral reefs in the Indo-Pacific Ocean, also exhibits enhanced resistance to both thermal and acid stress. To advance future studies, we report an improved high-quality genome assembly for A. intermedia obtained through PacBio Hi-Fi long-read sequencing, with a total size of 496.8 Mb. Compared to the previous version, our genome assembly shows substantial improvements in contiguity, with the Contig N50 increasing from 40.3 Kb to 2.9 Mb, and the number of contigs decreasing from 20,998 to 633. Specifically, our genome exhibits no undetectable ambiguous bases (N's) per 100 Kbp, which is remarkably lower than the previous version (5,276.11 per 100 Kbp). The percentage of assembly completeness evaluation based on Benchmarking Universal Single-Copy Orthologs (BUSCO) has increased from 90.6% to 92.6%. We predict a total of 26,852 protein-coding genes, with a BUSCO completeness of 95.7%, marking a 2.7% increase from the previous assembly. Our re-annotation and improved genome assembly of A. intermedia provide a valuable resource for further studies on coral adaptation mechanisms under climate change, and will facilitate comparative and evolutionary research of Acropora.
Related Topics
Concepts
Acropora
Coral
Biology
Coral reef
Genome
Contig
Reef
Anthozoa
Sequence assembly
Ecology
Evolutionary biology
Gene
Genetics
Transcriptome
Gene expression
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41597-025-05849-1
- https://www.nature.com/articles/s41597-025-05849-1.pdf
- OA Status
- gold
- References
- 59
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4413798027
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4413798027Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/s41597-025-05849-1Digital Object Identifier
- Title
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Re-annotation improved large-scale assembly of the reef-building coral Acropora intermediaWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-08-28Full publication date if available
- Authors
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Xinyao Chang, Wentao Han, Xiaomei Chen, C. J. Tang, Danyang Wang, Heng Huang, Yuli Li, Kai Chen, Jingjie Hu, Zhenmin Bao, Hong Chen, Shi WangList of authors in order
- Landing page
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https://doi.org/10.1038/s41597-025-05849-1Publisher landing page
- PDF URL
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https://www.nature.com/articles/s41597-025-05849-1.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://www.nature.com/articles/s41597-025-05849-1.pdfDirect OA link when available
- Concepts
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Acropora, Coral, Biology, Coral reef, Genome, Contig, Reef, Anthozoa, Sequence assembly, Ecology, Evolutionary biology, Gene, Genetics, Transcriptome, Gene expressionTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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59Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.with | 67, 87, 159 |
| abstract_inverted_index.(N's) | 116 |
| abstract_inverted_index.496.8 | 72 |
| abstract_inverted_index.90.6% | 148 |
| abstract_inverted_index.BUSCO | 161 |
| abstract_inverted_index.Hi-Fi | 64 |
| abstract_inverted_index.Kbp). | 131 |
| abstract_inverted_index.based | 138 |
| abstract_inverted_index.bases | 115 |
| abstract_inverted_index.coral | 31, 190 |
| abstract_inverted_index.lower | 123 |
| abstract_inverted_index.novel | 12 |
| abstract_inverted_index.reefs | 32 |
| abstract_inverted_index.shows | 82 |
| abstract_inverted_index.total | 69, 154 |
| abstract_inverted_index.under | 193 |
| abstract_inverted_index.which | 120 |
| abstract_inverted_index.(Brook | 21 |
| abstract_inverted_index.1891), | 22 |
| abstract_inverted_index.20,998 | 105 |
| abstract_inverted_index.26,852 | 156 |
| abstract_inverted_index.92.6%. | 150 |
| abstract_inverted_index.95.7%, | 164 |
| abstract_inverted_index.Contig | 89 |
| abstract_inverted_index.Ocean, | 36 |
| abstract_inverted_index.PacBio | 63 |
| abstract_inverted_index.future | 49 |
| abstract_inverted_index.genes, | 158 |
| abstract_inverted_index.genome | 56, 80, 110, 177 |
| abstract_inverted_index.marine | 8 |
| abstract_inverted_index.number | 100 |
| abstract_inverted_index.report | 52 |
| abstract_inverted_index.(BUSCO) | 144 |
| abstract_inverted_index.advance | 48 |
| abstract_inverted_index.change, | 195 |
| abstract_inverted_index.climate | 194 |
| abstract_inverted_index.contigs | 102 |
| abstract_inverted_index.corals, | 1 |
| abstract_inverted_index.further | 187 |
| abstract_inverted_index.habitat | 5 |
| abstract_inverted_index.marking | 165 |
| abstract_inverted_index.predict | 152 |
| abstract_inverted_index.primary | 2 |
| abstract_inverted_index.provide | 182 |
| abstract_inverted_index.stress. | 46 |
| abstract_inverted_index.studies | 188 |
| abstract_inverted_index.thermal | 43 |
| abstract_inverted_index.through | 62 |
| abstract_inverted_index.version | 127 |
| abstract_inverted_index.vibrant | 28 |
| abstract_inverted_index.Acropora | 0, 19 |
| abstract_inverted_index.Compared | 74 |
| abstract_inverted_index.assembly | 57, 81, 135, 178 |
| abstract_inverted_index.changes. | 18 |
| abstract_inverted_index.enhanced | 39 |
| abstract_inverted_index.exhibits | 38, 111 |
| abstract_inverted_index.improved | 54, 176 |
| abstract_inverted_index.increase | 168 |
| abstract_inverted_index.numerous | 7 |
| abstract_inverted_index.obtained | 61 |
| abstract_inverted_index.previous | 77, 126, 171 |
| abstract_inverted_index.research | 202 |
| abstract_inverted_index.resource | 185 |
| abstract_inverted_index.species, | 9 |
| abstract_inverted_index.studies, | 50 |
| abstract_inverted_index.survival | 13 |
| abstract_inverted_index.valuable | 184 |
| abstract_inverted_index.version, | 78 |
| abstract_inverted_index.(5,276.11 | 128 |
| abstract_inverted_index.Acropora. | 204 |
| abstract_inverted_index.Orthologs | 143 |
| abstract_inverted_index.Universal | 141 |
| abstract_inverted_index.ambiguous | 114 |
| abstract_inverted_index.assembly. | 172 |
| abstract_inverted_index.increased | 146 |
| abstract_inverted_index.long-read | 65 |
| abstract_inverted_index.pressures | 14 |
| abstract_inverted_index.providing | 4 |
| abstract_inverted_index.adaptation | 191 |
| abstract_inverted_index.decreasing | 103 |
| abstract_inverted_index.ecosystems | 29 |
| abstract_inverted_index.evaluation | 137 |
| abstract_inverted_index.facilitate | 198 |
| abstract_inverted_index.increasing | 91 |
| abstract_inverted_index.intermedia | 20, 60, 181 |
| abstract_inverted_index.mechanisms | 192 |
| abstract_inverted_index.percentage | 133 |
| abstract_inverted_index.remarkably | 122 |
| abstract_inverted_index.resistance | 40 |
| abstract_inverted_index.Single-Copy | 142 |
| abstract_inverted_index.comparative | 199 |
| abstract_inverted_index.contiguity, | 86 |
| abstract_inverted_index.contributor | 25 |
| abstract_inverted_index.sequencing, | 66 |
| abstract_inverted_index.significant | 24 |
| abstract_inverted_index.substantial | 83 |
| abstract_inverted_index.Benchmarking | 140 |
| abstract_inverted_index.Indo-Pacific | 35 |
| abstract_inverted_index.completeness | 136, 162 |
| abstract_inverted_index.evolutionary | 201 |
| abstract_inverted_index.high-quality | 55 |
| abstract_inverted_index.improvements | 84 |
| abstract_inverted_index.undetectable | 113 |
| abstract_inverted_index.Specifically, | 108 |
| abstract_inverted_index.environmental | 17 |
| abstract_inverted_index.re-annotation | 174 |
| abstract_inverted_index.reef-builders | 3 |
| abstract_inverted_index.protein-coding | 157 |
| cited_by_percentile_year | |
| corresponding_author_ids | https://openalex.org/A5101202941 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 12 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/14 |
| sustainable_development_goals[0].score | 0.7400000095367432 |
| sustainable_development_goals[0].display_name | Life below water |
| citation_normalized_percentile.value | 0.39007705 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |