Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 378

The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.

The Sinocyclocheilus cavefish genome provides insights into cave adaptation

Open access
Yang, Junxing, Chen, Xiaoli, Bai, Jie, Fang, Dongming, Qiu, Ying, Jiang, Wansheng, Yuan, Hui, Bian, Chao, Lu, Jiang, He, Shiyang, Pan, Xiaofu, Zhang, Yaolei, Wang, Xiaoai, You, Xinxin, Wang, Yongsi, Sun, Ying, Mao, Danqing, Liu, Yong, Fan, Guangyi, Zhang, He, Chen, Xiaoyong, Zhang, Xinhui, Zheng, Lanping, Wang, Jintu, Cheng, Le, Chen, Jieming, Ruan, Zhiqiang, Li, Jia, Yu, Hui, Peng, Chao, Ma, Xingyu, Xu, Junmin, He, You, Xu, Zhengfeng, Xu, Pao, Wang, Jian, Yang, Huanming, Wang, Jun, Whitten, Tony, Xu, Xun, Shi, Qiong·2016·BMC Biology
DOI 10.1186/s12915-015-0223-4
Open this paper in CoChat — free account

Abstract

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1186/s12915-015-0223-4

Cites

11 of 11 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 11 references

Cited by

See all 378

Metadata

Authors
Yang, J., Chen, X., Bai, J., Fang, D., Qiu, Y., Jiang, W., Yuan, H., Bian, C., Lu, J., He, S., Pan, X., Zhang, Y., Wang, X., You, X., Wang, Y., Sun, Y., Mao, D., Liu, Y., Fan, G., Zhang, H., Chen, X., Zhang, X., Zheng, L., Wang, J., Cheng, L., Chen, J., Ruan, Z., Li, J., Yu, H., Peng, C., Ma, X., Xu, J., He, Y., Xu, Z., Xu, P., Wang, J., Yang, H., Wang, J., Whitten, T., Xu, X., & Shi, Q.
Venue
BMC Biology
Publisher
Springer Science and Business Media LLC
Published
2016-01-04
Volume
14
Issue
1
Pages
1-1
ISSN
1741-7007 (ISSN-L)
DOI
10.1186/s12915-015-0223-4
OpenAlex
W2232237847
Cited by
378
References
11
FWCI
33.97
Type
journal article
Language
en
Open access
gold

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: The Sinocyclocheilus cavefish genome provides insights into cave adaptation. https://app.cochat.ai/papers/10.1186/s12915-015-0223-4
The paper
Yang, J., Chen, X., Bai, J., Fang, D., Qiu, Y., Jiang, W., Yuan, H., Bian, C., Lu, J., He, S., Pan, X., Zhang, Y., Wang, X., You, X., Wang, Y., Sun, Y., Mao, D., Liu, Y., Fan, G., . . . Shi, Q. (2016). The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biology. https://doi.org/10.1186/s12915-015-0223-4

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.