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Genome analysis of the rice coral Montipora capitata

Published on Feb 22, 2019in Scientific Reports 4.12
· DOI :10.1038/s41598-019-39274-3
Alexander Shumaker1
Estimated H-index: 1
(Rutgers University),
Hollie M. Putnam21
Estimated H-index: 21
(University of Rhode Island)
+ 7 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(Rutgers University)
Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai’i. Our work provides insights into the architecture of coral genomes and shows how they differ in size and gene inventory, putatively due to population size variation. We describe a recent example of foreign gene acquisition via a bacterial gene transfer agent and illustrate the major pathways of stress response that can be used to predict regulatory components of the transcriptional networks in M. capitata. These genomic resources provide insights into the adaptive potential of these sessile, long-lived species in both natural and human influenced environments and facilitate functional and population genomic studies aimed at Hawaiian reef restoration and conservation.
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Published on Dec 1, 2015in Mobile Dna 5.89
Weidong Bao8
Estimated H-index: 8
(Genetic Information Research Institute),
Kenji Kojima25
Estimated H-index: 25
(University of Tokyo),
Oleksiy Kohany11
Estimated H-index: 11
(Genetic Information Research Institute)
Repbase Update (RU) is a database of representative repeat sequences in eukaryotic genomes. Since its first development as a database of human repetitive sequences in 1992, RU has been serving as a well-curated reference database fundamental for almost all eukaryotic genome sequence analyses. Here, we introduce recent updates of RU, focusing on technical issues concerning the submission and updating of Repbase entries and will give short examples of using RU data. RU sincerely invites a broader ...
341 Citations Source Cite
Published on Aug 19, 2004in BMC Bioinformatics 2.21
Robert C. Edgar17
Estimated H-index: 17
(University of California, Berkeley)
Background In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed f...
4,154 Citations Source Cite
Published on May 1, 1977in Archives of Biochemistry and Biophysics 3.12
Marc Solioz40
Estimated H-index: 40
(Saint Louis University),
Barry Marrs16
Estimated H-index: 16
(Saint Louis University)
Abstract Photosynthetic bacteria of the species Rhodopseudomonas capsulata are capable of exchanging genetic information via a recently discovered gene transfer agent (GTA). The 70S particle mediating the genetic exchange was purified and its nucleic acid was analyzed. Cell-free filtrates containing GTA were prepared by filtration of stationary cultures of R. capsulata on an Amicon thin-channel filtration apparatus. Purification of this filtrate was achieved by successive membrane filtration, di...
68 Citations Source Cite
Published on Dec 1, 2015in Genome Biology 13.21
David Emms8
Estimated H-index: 8
(University of Oxford),
Steven L. Kelly54
Estimated H-index: 54
(University of Oxford)
Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by pro...
377 Citations Source Cite
Published on Dec 1, 2008in BMC Bioinformatics 2.21
Peter Langfelder22
Estimated H-index: 22
(University of California, Los Angeles),
Steve Horvath87
Estimated H-index: 87
(University of California, Los Angeles)
Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and ...
2,812 Citations Source Cite
Published on Nov 1, 2010in Developmental and Comparative Immunology 2.91
E. Charlotte E. Kvennefors6
Estimated H-index: 6
(University of Queensland),
William Leggat25
Estimated H-index: 25
(James Cook University)
+ 3 AuthorsAndrew C. Barnes27
Estimated H-index: 27
(University of Queensland)
Reef-building corals are representatives of one of the earliest diverging metazoan lineages and are experiencing increases in bleaching events (breakdown of the coral-Symbiodinium symbiosis) and disease outbreaks. The present study investigates the roles of two pattern recognition proteins, the mannose binding lectin Millectin and a complement factor C3-like protein (C3-Am), in the coral Acropora millepora. The results indicate that the innate immune functions of these molecules are conserved an...
55 Citations Source Cite
Published on Nov 1, 2007in Aquatic Toxicology 3.88
Carys L. Mitchelmore17
Estimated H-index: 17
(University of Maryland Center for Environmental Science),
E. Alan Verde5
Estimated H-index: 5
(Maine Maritime Academy),
Virginia M. Weis35
Estimated H-index: 35
(Oregon State University)
Abstract Coral-reef ecosystems are increasingly being impacted by a wide variety of anthropogenic inputs, including heavy metals, which could be contributing to coral reef stress and bleaching episodes. Fragments of Pocillopora damicornis were exposed in the laboratory to cadmium (Cd) or copper (Cu) chlorides (0, 5, 50 μg l −1 ) for 14 days and analyzed for metal content in the whole association, algal or animal fractions. Various physiological and biochemical parameters were also measured, such...
45 Citations Source Cite
Published on Mar 1, 2010in Genomics, Proteomics & Bioinformatics
Dapeng Wang11
Estimated H-index: 11
(Chinese Academy of Sciences),
Yubin Zhang2
Estimated H-index: 2
(Chinese Academy of Sciences)
+ 2 AuthorsJun Yu65
Estimated H-index: 65
(Chinese Academy of Sciences)
We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous vers...
188 Citations Source Cite
Published on Mar 1, 2015in Marine Biology 2.21
Emma M. Gibbin6
Estimated H-index: 6
(Victoria University of Wellington),
Hollie M. Putnam21
Estimated H-index: 21
(University of Hawaii)
+ 2 AuthorsSimon K. Davy26
Estimated H-index: 26
(Victoria University of Wellington)
It is widely acknowledged that temperature stress affects an organism’s sensitivity to ocean acidification and vice versa, yet it is not clear how the two are mechanistically linked. Here, we induced thermal stress in two coral species with differing bleaching susceptibilities to measure how a reduction in photosynthetic performance impacts intracellular pH (pHi) regulation in the symbiotic dinoflagellates (Symbiodinium sp.) and their host coral cells. Our hypothesis was that thermally induced p...
8 Citations Source Cite
Published on Jul 1, 2006in Nucleic Acids Research 11.56
Mario Stanke36
Estimated H-index: 36
Oliver Keller6
Estimated H-index: 6
+ 3 AuthorsBurkhard Morgenstern36
Estimated H-index: 36
AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most existing gene finders, the first version of AUGUSTUS returned one transcript per predicted gene and ignored the phenomenon of alternative splicing. Herein, we present a WWW server for an extended version of AUGUSTUS that is able to predict multiple splice variants. To our knowledge, this is the first ab initio gene finder ...
378 Citations Source Cite
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