Evidence map›Paper›PMID 30050104›Full record

ArticleScientific reports2018

The habu genome reveals accelerated evolution of venom protein genes.

Hiroki Shibata, Takahito Chijiwa, Naoko Oda-Ueda, Hitomi Nakamura, Kazuaki Yamaguchi, Shousaku Hattori, Kazumi Matsubara, Yoichi Matsuda, Akifumi Yamashita, Akiko Isomoto and 14 more

Abstract read
In one paragraph

Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.

0numbers the graph read from it
0cells of the map it votes in
47citing 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

47 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Genome of venomous caterpillarProceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  5. Review
  6. Article
  7. Review
  8. Review
  9. Article
  10. Article
  11. Article
  12. Toxins · 2023
    Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. 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

24 authors.

Hiroki ShibataDivision of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. hshibata@gen.kyushu-u.ac.jp.
Takahito ChijiwaDepartment of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, 860-0082, Japan.
Naoko Oda-UedaDepartment of Biochemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.
Hitomi NakamuraDepartment of Biochemistry, Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.
Kazuaki YamaguchiDepartment of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, 860-0082, Japan.
Shousaku HattoriInstitute of Medical Science, University of Tokyo, Oshima-gun, Kagoshima, 894-1531, Japan.
Kazumi MatsubaraDepartment of Information and Biological Sciences, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Aichi, 467-0802, Japan.
Yoichi MatsudaDepartment of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
Akifumi YamashitaDepartment of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
Akiko IsomotoDivision of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
Kazuki MoriGraduate School of Systems Life Sciences, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan.
Kosuke TashiroGraduate School of Systems Life Sciences, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan.
Satoru KuharaGraduate School of Systems Life Sciences, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, 812-8581, Japan.
Shinichi YamasakiDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Manabu FujieDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Hiroki GotoDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Ryo KoyanagiDNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Takeshi TakeuchiMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Yasuyuki FukumakiDivision of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
Motonori OhnoDepartment of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, 860-0082, Japan.
Eiichi ShoguchiMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Kanako HisataMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
Noriyuki SatohMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. norisky@oist.jp.ORCID 0000-0002-4480-3572
Tomohisa OgawaDepartment of Biomolecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan. tomohisa.ogawa.c3@tohoku.ac.jp.ORCID 0000-0001-8700-6330

Funding

Ministry of Education, Culture, Sports, Science, and Technology (MEXT) 18H02498Ministry of Education, Culture, Sports, Science, and Technology (MEXT) 23107505
6 · The paper itself

Abstract

Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition.

Indexed as

Evolution, MolecularAnimalsGene DuplicationPhylogenyReptilian ProteinsSequence Analysis, DNASnake VenomsTrimeresurusReptilian ProteinsSnake Venoms

Identifiers

PMID30050104
PMCPMC6062510

What OpenQuestion holds

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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.