Evidence map›Paper›PMID 39557846›Full record

ArticleScientific data2024

Chromosome-level genome assembly and annotation of the tropical sea cucumber Stichopus monotuberculatus.

Ting Chen, Yun Yang, Xuan Wang, Zhou Qin, Zhenyu Xie, Dingding Fan, Chunhua Ren, Hongyan Sun, Peng Luo, Xiao Jiang and 14 more

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
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.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

Ting Chen *Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Yun Yang *Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
Xuan WangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Zhou QinKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Zhenyu XieLaboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, China.
Dingding FanKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.ORCID 0000-0002-8201-3846
Chunhua RenKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Hongyan SunGuangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
Peng LuoKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Xiao JiangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Hao LongLaboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, 570228, China.
Chang ChenKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Wenjie PanKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Zixuan EKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Jiasheng HuangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Qianying HuangSchool of Medicine, Foshan University, Foshan, 528225, China.
Jianfeng XuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Zepeng ZhangGuangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, China.
Chuhang ChengGuangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, 530007, China.
Suzhong YuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Yanhong WangKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
Fajun JiangGuangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, Nanning, 530007, China.
Aifen YanSchool of Medicine, Foshan University, Foshan, 528225, China. yanaifen@fosu.edu.cn.
Chaoqun HuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China. hucq@scsio.ac.cn.

Funding

Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province) 2024A1515010899Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province) 2024A1515011418Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology) 2022YFD2401301National Natural Science Foundation of China (National Science Foundation of China) 42176132
6 · The paper itself

Abstract

In this study, a chromosome-level genome of the tropical sea cucumber Stichopus monotuberculatus was generated by a combination of Nanopore long-read, Illumina short-read, and Hi-C sequencing technologies. The final assembly was 810.54 Mb in length, with contig N50 and scaffold N50 values of 10.15 Mb and 35.36 Mb, respectively. This assembly comprised 23 pseudo-chromosomes, covering 99.82% of the genome. Completeness analysis using BUSCO indicated that 97.8% of the metazoan conserved genes were presented in their entirety. A total of 29,596 protein-coding genes were predicted, with functional annotations available for 94.43% of these genes. The high-quality genome assembly produced in this study may provide an essential foundation for future researches on resource conservation and genetic breeding of S. monotuberculatus.

Indexed as

ChromosomesGenomeMolecular Sequence AnnotationAnimalsStichopus

Identifiers

PMID39557846
PMCPMC11574266

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