Evidence map›Paper›PMID 36639248›Full record

ArticleG3 (Bethesda, Md.)2023

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination.

Mark A Arick, Corrinne E Grover, Chuan-Yu Hsu, Zenaida Magbanua, Olga Pechanova, Emma R Miller, Adam Thrash, Ramey C Youngblood, Lauren Ezzell, Md Samsul Alam and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Review
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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

15 authors.

Mark A ArickInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.ORCID 0000-0002-7207-3052
Corrinne E GroverEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA.
Chuan-Yu HsuInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Zenaida MagbanuaInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Olga PechanovaInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Emma R MillerEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA.
Adam ThrashInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Ramey C YoungbloodInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Lauren EzzellInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Md Samsul AlamDepartment of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
John A H BenzieWorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia.
Matthew G HamiltonWorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia.
Attila KarsiDepartment of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
Mark L LawrenceGlobal Center for Aquatic Health and Food Security, Mississippi State University, Mississippi State, MS 39762, USA.
Daniel G PetersonInstitute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

Indexed as

CarpsCyprinidaeAnimalsChromosomesGene FlowGenome SizeHumansaquacultureddRAD-seqgenomerohuruisex determination

Identifiers

PMID36639248
PMCPMC9997561

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Registered trials

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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.