Evidence map›Paper›PMID 38909036›Full record

ArticleScientific data2024

Integrating Iso-seq and RNA-seq data for the reannotation of the greater amberjack genome.

Yuanli Zhao, Zonggui Chen, Meidi Hu, Hairong Liu, Haiping Zhao, Yang Huang, Mouyan Jiang, Shengkang Li, Guangli Li, Chunhua Zhu and 2 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 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
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

12 authors.

Yuanli Zhao *Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
Zonggui Chen *Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
Meidi Hu *Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.ORCID 0000-0001-6177-4606
Hairong LiuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
Haiping ZhaoKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China.
Yang HuangChina Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China.
Mouyan JiangFisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
Shengkang LiGuangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou, 515063, China.
Guangli LiFisheries College of Guangdong Ocean University, Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China.
Chunhua ZhuChina Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524025, China. zhu860025@163.com.
Wei HuKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China. huwei@ihb.ac.cn.
Daji LuoKey Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, The Innovative Academy of Seed Design, Hubei Hongshan Laboratory, Guangdong Laboratory for Lingnan Modern Agriculture, Chinese Academy of Sciences, Wuhan, 430072, China. luodaji@ihb.ac.cn.ORCID 0000-0002-8051-9624

Funding

National Natural Science Foundation of China (National Science Foundation of China) No. 31922085
6 · The paper itself

Abstract

The greater amberjack is a very important fishery species with high commercial value, and it is distributed worldwide. Transcriptome-based studies on S. dumerili have been limited by an inadequate reference genome and a lack of well-annotated full-length transcripts. In this study, a total of 12 tissues from juvenile and adult fish both sexes were collected for next-generation RNA sequencing (RNA-seq) and full-length isoform sequencing (Iso-seq). For Iso-seq, a total of 163,218, 149,716, and 189,169 high-quality unique transcript sequences were obtained, with an N50 of 5,441, 5,255, and 5,939, from juvenile, adult male and adult female S. dumerili, respectively. We integrated the Iso-seq and RNA-seq data to construct a comprehensive gene annotation and systematically profiled the dynamics of gene expression across the 12 tissues. Our gene models had greater detail and accuracy than those from NCBI and Ensembl, with more precise polyA locations. These resources serve as a foundation for functional genomic studies and provide valuable insights into the molecular mechanisms underlying the development, reproduction and commercial traits of amberjack.

Indexed as

GenomeRNA-SeqAnimalsFemaleFishesHigh-Throughput Nucleotide SequencingMaleMolecular Sequence AnnotationSequence Analysis, RNATranscriptome

Identifiers

PMID38909036
PMCPMC11193819

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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.