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Genome analysis of the rice coral Montipora capitata

Published on Feb 22, 2019in Scientific Reports 4.01
· DOI :10.1038/s41598-019-39274-3
Alexander Shumaker1
Estimated H-index: 1
(RU: Rutgers University),
Hollie M. Putnam24
Estimated H-index: 24
(URI: University of Rhode Island)
+ 7 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
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Abstract
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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References79
Newest
Published on Dec 1, 2018in Scientific Reports 4.01
Ross Cunning13
Estimated H-index: 13
(UM: University of Miami),
Rachael A. Bay8
Estimated H-index: 8
(UC Davis: University of California, Davis)
+ 2 AuthorsNikki Traylor-Knowles12
Estimated H-index: 12
(UM: University of Miami)
Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as ...
John R. Pringle67
Estimated H-index: 67
(Stanford University),
Marie E. Strader5
Estimated H-index: 5
(University of Texas at Austin)
+ 2 AuthorsPhillip A. Clevesa1
Estimated H-index: 1
(University of Texas at Austin)
We thank S. Sanders, B. Mason, and B. Fu for helpful suggestions on the design of the sgRNAs; H. Elder and I. Bjornsbo for valuable assistance during coral spawning; and Eppendorf South Pacific for loan of the microinjection system. MiSeq sequencing was performed by the Genomic Sequencing and Analysis Facility at the University of Texas at Austin. Some bioinformatic analyses were carried out using the computational resources of the Texas Advanced Computing Center. Funding for this study was prov...
Published on Feb 22, 2018in bioRxiv
Yi Jin Liew8
Estimated H-index: 8
(KAUST: King Abdullah University of Science and Technology),
Emily J. Howells13
Estimated H-index: 13
(NYUAD: New York University Abu Dhabi)
+ 4 AuthorsManuel Aranda24
Estimated H-index: 24
(KAUST: King Abdullah University of Science and Technology)
We thank D. Abrego, G. Vaughan, and D. McParland for assistance with fieldwork, coral spawning, and the collection of environmental data, as well as the KAUST Sequencing Core Facility for the sequencing of the libraries. This work was financially supported by KAUST (sequencing and bioinformatics) and NYUAD (fieldwork and coral spawning).
Published on Jan 1, 2018in Genome Biology and Evolution 3.73
Dennis Versluis4
Estimated H-index: 4
(WUR: Wageningen University and Research Centre),
Bart Nijsse4
Estimated H-index: 4
(WUR: Wageningen University and Research Centre)
+ 7 AuthorsDetmer Sipkema20
Estimated H-index: 20
(WUR: Wageningen University and Research Centre)
Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways...
Published on Dec 18, 2017in Ecology 4.29
T. P. Hughes48
Estimated H-index: 48
(JCU: James Cook University),
James T. Kerry7
Estimated H-index: 7
(JCU: James Cook University),
T. Simpson1
Estimated H-index: 1
Published on Oct 1, 2017in Genomics 3.16
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University),
Ehud Zelzion10
Estimated H-index: 10
(RU: Rutgers University)
+ 4 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
Abstract Stony coral (Scleractinia) genomes are still poorly explored and many questions remain about their evolution and contribution to the success and longevity of reefs. We analyzed transcriptome and genome data from Montipora capitata , Acropora digitifera , and transcriptome data from 20 other coral species. To our surprise, we found highly conserved, anciently derived, Scleractinia COral-specific Repeat families (SCORs) that are abundant in all the studied lineages. SCORs form complex sec...
Published on Oct 1, 2017in Nature Ecology and Evolution
Kenneth R. N. Anthony35
Estimated H-index: 35
(Australian Institute of Marine Science),
Line K. Bay20
Estimated H-index: 20
(Australian Institute of Marine Science)
+ 15 AuthorsTom Moore3
Estimated H-index: 3
(NOAA: National Oceanic and Atmospheric Administration)
We anticipate that conventional management approaches will be insufficient to protect coral reefs, even if global warming is limited to 1.5 °C. Emerging technologies are needed to stem the decline of these natural assets.
Published on Oct 1, 2017in Cellular Microbiology 4.29
Vincent Dani4
Estimated H-index: 4
,
Fabrice Priouzeau4
Estimated H-index: 4
+ 5 AuthorsCécile Sabourault5
Estimated H-index: 5
The symbiotic interaction between cnidarians (e.g. corals and sea anemones) and photosynthetic dinoflagellates of the genus Symbiodinium is triggered by both host-symbiont recognition processes and metabolic exchange between the two partners. The molecular communication is crucial for homeostatic regulation of the symbiosis, both under normal conditions and during stresses that further lead to symbiosis collapse. It is therefore important to identify and fully characterize the key players of thi...
Published on Sep 29, 2017in Annual Review of Virology 6.57
Andrew S. Lang25
Estimated H-index: 25
,
Alexander B. Westbye6
Estimated H-index: 6
,
J. Thomas Beatty30
Estimated H-index: 30
Diverse prokaryotes produce gene transfer agents (GTAs), which are bacteriophage-like particles that exclusively package pieces of the producing cell's genome and transfer them to other cells. There are clear evolutionary connections between GTAs and phages, but GTAs have properties that lead us to suggest they are more than simply defective phages and instead provide a selective advantage for the producing organisms. The five types of currently known GTAs are genetically distinct, indicating mu...
Published on Sep 1, 2017in Global Change Biology 8.88
Madeleine J. H. van Oppen44
Estimated H-index: 44
(University of Melbourne),
Ruth D. Gates44
Estimated H-index: 44
+ 19 AuthorsHannah E. Epstein3
Estimated H-index: 3
Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine-protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and ...
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Newest
Published in BMC Evolutionary Biology 3.04
Regina L. Cunha11
Estimated H-index: 11
(University of the Algarve),
Zac H. Forsman16
Estimated H-index: 16
+ -3 AuthorsRobert J. Toonen41
Estimated H-index: 41
Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with wide...
Published on Jun 27, 2019in Genome Biology and Evolution 3.73
Martin Helmkampf16
Estimated H-index: 16
(UH Hilo: University of Hawaii at Hilo),
M. Renee Bellinger11
Estimated H-index: 11
(UH Hilo: University of Hawaii at Hilo)
+ 2 AuthorsMisaki Takabayashi4
Estimated H-index: 4
(UH Hilo: University of Hawaii at Hilo)