Evidence map›Paper›PMID 40877298›Full record

ArticleScientific data2025

Re-annotation improved large-scale assembly of the reef-building coral Acropora intermedia.

Xinyao Chang, Wentao Han, Xiaomei Chen, Caiyin Tang, Danyang Wang, Heng Huang, Yuli Li, Kai Chen, Jingjie Hu, Zhenmin Bao and 2 more

Abstract read
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Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Xinyao Chang *Key Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Wentao Han *Key Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.ORCID 0000-0003-1423-3975
Xiaomei ChenKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Caiyin TangKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Danyang WangSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.ORCID 0009-0007-2366-7923
Heng HuangKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Yuli LiKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Kai ChenSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.ORCID 0000-0001-7230-6488
Jingjie HuKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Zhenmin BaoKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China.
Hong ChenHainan South China Sea of Institute Tropical Oceanography, Sanya, China. chenhong68@vip.163.com.
Shi WangKey Laboratory of Tropical Aquatic Germplasm of Hainan Province & Fang Zongxi Center for Marine Evo-Devo, MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Sanya, Qingdao, China. swang@ouc.edu.cn.ORCID 0000-0002-9571-9864

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

AnthozoaGenomeMolecular Sequence AnnotationAnimalsCoral Reefs

Identifiers

PMID40877298
PMCPMC12394630

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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.