Literature DB >> 31882190

Unknown to Known: Advancing Knowledge of Coral Gene Function.

Phillip A Cleves1, Alexander Shumaker2, JunMo Lee3, Hollie M Putnam4, Debashish Bhattacharya5.   

Abstract

Given the catastrophic changes befalling coral reefs, understanding coral gene function is essential to advance reef conservation. This has proved challenging due to the paucity of genomic data and genetic tools available for corals. Recently, CRISPR/Cas9 gene editing was applied to these species; however, a major bottleneck is the identification and prioritization of candidate genes for manipulation. This issue is exacerbated by the many unknown ('dark') coral genes that may play key roles in the stress response. We review the use of gene coexpression networks that incorporate both known and unknown genes to identify targets for reverse genetic analysis. This approach also provides a framework for the annotation of dark genes in established interaction networks to improve our fundamental knowledge of coral gene function.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Keywords:  coexpression network; coral bleaching; genome editing; multiomics; thermal stress

Mesh:

Year:  2019        PMID: 31882190     DOI: 10.1016/j.tig.2019.11.001

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  8 in total

1.  Insights into coral bleaching under heat stress from analysis of gene expression in a sea anemone model system.

Authors:  Phillip A Cleves; Cory J Krediet; Erik M Lehnert; Masayuki Onishi; John R Pringle
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-09       Impact factor: 11.205

2.  A breakthrough in understanding the molecular basis of coral heat tolerance.

Authors:  Madeleine J H van Oppen; John G Oakeshott
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-09       Impact factor: 11.205

3.  Transcriptome analysis provides a blueprint of coral egg and sperm functions.

Authors:  Julia Van Etten; Alexander Shumaker; Tali Mass; Hollie M Putnam; Debashish Bhattacharya
Journal:  PeerJ       Date:  2020-08-18       Impact factor: 2.984

4.  A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity.

Authors:  Shani Levy; Anamaria Elek; Xavier Grau-Bové; Simón Menéndez-Bravo; Marta Iglesias; Amos Tanay; Tali Mass; Arnau Sebé-Pedrós
Journal:  Cell       Date:  2021-05-03       Impact factor: 41.582

5.  Investigating calcification-related candidates in a non-symbiotic scleractinian coral, Tubastraea spp.

Authors:  Laura Capasso; Manuel Aranda; Guoxin Cui; Melanie Pousse; Sylvie Tambutté; Didier Zoccola
Journal:  Sci Rep       Date:  2022-08-06       Impact factor: 4.996

6.  A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations.

Authors:  Hao Jia; Sung-Joon Park; Kenta Nakai
Journal:  BMC Bioinformatics       Date:  2021-06-02       Impact factor: 3.307

7.  Caspases from scleractinian coral show unique regulatory features.

Authors:  Suman Shrestha; Jessica Tung; Robert D Grinshpon; Paul Swartz; Paul T Hamilton; Bradford Dimos; Laura Mydlarz; A Clay Clark
Journal:  J Biol Chem       Date:  2020-08-11       Impact factor: 5.157

8.  Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis.

Authors:  Duckhyun Lhee; JunMo Lee; Khaoula Ettahi; Chung Hyun Cho; Ji-San Ha; Ya-Fan Chan; Udi Zelzion; Timothy G Stephens; Dana C Price; Arwa Gabr; Eva C M Nowack; Debashish Bhattacharya; Hwan Su Yoon
Journal:  Mol Biol Evol       Date:  2021-01-23       Impact factor: 16.240

  8 in total

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