1
|
Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of 2 high-quality columbid reference genomes from sequencing of a Columba livia × Columba guinea F1 hybrid. G3 (Bethesda) 2024; 14:jkad280. [PMID: 38066578 PMCID: PMC10849363 DOI: 10.1093/g3journal/jkad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for columbids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for 2 columbid species, Columba livia and Columba guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
Collapse
Affiliation(s)
- Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA 94025, USA
- Digital BioLogic d.o.o, Ivanić-Grad 10310, Croatia
| | - Anna I Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
2
|
Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F 1 hybrid. bioRxiv 2023:2023.10.11.561892. [PMID: 37873124 PMCID: PMC10592783 DOI: 10.1101/2023.10.11.561892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Pigeons and doves (family Columbidae) are one of the most diverse extant avian lineages, and many species have served as key models for evolutionary genomics, developmental biology, physiology, and behavioral studies. Building genomic resources for colubids is essential to further many of these studies. Here, we present high-quality genome assemblies and annotations for two columbid species, Columba livia and C. guinea. We simultaneously assembled C. livia and C. guinea genomes from long-read sequencing of a single F1 hybrid individual. The new C. livia genome assembly (Cliv_3) shows improved completeness and contiguity relative to Cliv_2.1, with an annotation incorporating long-read IsoSeq data for more accurate gene models. Intensive selective breeding of C. livia has given rise to hundreds of breeds with diverse morphological and behavioral characteristics, and Cliv_3 offers improved tools for mapping the genomic architecture of interesting traits. The C. guinea genome assembly is the first for this species and is a new resource for avian comparative genomics. Together, these assemblies and annotations provide improved resources for functional studies of columbids and avian comparative genomics in general.
Collapse
Affiliation(s)
- Emily T. Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Carson Holt
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Ivan Sović
- Pacific Biosciences, Menlo Park, CA, USA
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Anna I. Vickrey
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
3
|
Kronenberg ZN, Rhie A, Koren S, Concepcion GT, Peluso P, Munson KM, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat Commun 2021; 12:1935. [PMID: 33911078 PMCID: PMC8081726 DOI: 10.1038/s41467-020-20536-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/12/2020] [Indexed: 01/27/2023] Open
Abstract
Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80-91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.
Collapse
Affiliation(s)
- Zev N Kronenberg
- Phase Genomics, Seattle, WA, USA.
- Pacific Biosciences, Menlo Park, CA, USA.
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kristen Kuhn
- US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA
| | | | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Olivier Fedrigo
- Vertebrate Genomes Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, 29122, Piacenza, Italy
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | |
Collapse
|
4
|
Soifer L, Fong NL, Yi N, Ireland AT, Lam I, Sooknah M, Paw JS, Peluso P, Concepcion GT, Rank D, Hastie AR, Jojic V, Ruby JG, Botstein D, Roy MA. Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual. G3 (Bethesda) 2020; 10:2911-2925. [PMID: 32631951 PMCID: PMC7466960 DOI: 10.1534/g3.119.400995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
Abstract
In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which polymorphisms are detected but not assigned to one or the other of the homologous chromosomes. Yet chromosomal phase information is invaluable for the understanding of phenotypic trait inheritance in the cases of compound heterozygosity, allele-specific expression or cis-acting variants. Here we use a combination of tools and sequencing technologies to generate a de novo diploid assembly of the human primary cell line WI-38. First, data from PacBio single molecule sequencing and Bionano Genomics optical mapping were combined to generate an unphased assembly. Next, 10x Genomics linked reads were combined with the hybrid assembly to generate a partially phased assembly. Lastly, we developed and optimized methods to use short-read (Illumina) sequencing of flow cytometry-sorted metaphase chromosomes to provide phase information. The final genome assembly was almost fully (94%) phased with the addition of approximately 2.5-fold coverage of Illumina data from the sequenced metaphase chromosomes. The diploid nature of the final de novo genome assembly improved the resolution of structural variants between the WI-38 genome and the human reference genome. The phased WI-38 sequence data are available for browsing and download at wi38.research.calicolabs.com. Our work shows that assembling a completely phased diploid genome de novo from the DNA of a single individual is now readily achievable.
Collapse
Affiliation(s)
- Llya Soifer
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nicole L Fong
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Nelda Yi
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | - Irene Lam
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | | | | | | - David Rank
- Pacific Biosciences, Menlo Park, CA 94025
| | | | | | - J Graham Ruby
- Calico Life Sciences LLC, South San Francisco, CA 94080
| | | | | |
Collapse
|
5
|
Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 2019; 37:1155-1162. [PMID: 31406327 PMCID: PMC6776680 DOI: 10.1038/s41587-019-0217-9] [Citation(s) in RCA: 745] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022]
Abstract
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Jana Ebler
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
| | | | | | - Nathan D Olson
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Gene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Heng Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | |
Collapse
|
6
|
Bachvaroff TR, Gornik SG, Concepcion GT, Waller RF, Mendez GS, Lippmeier JC, Delwiche CF. Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades. Mol Phylogenet Evol 2013; 70:314-22. [PMID: 24135237 DOI: 10.1016/j.ympev.2013.10.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 09/24/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these 'protist' taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates.
Collapse
Affiliation(s)
- Tsvetan R Bachvaroff
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd., Edgewater, MD 21037, United States.
| | | | | | | | | | | | | |
Collapse
|
7
|
Padilla-Gamiño JL, Pochon X, Bird C, Concepcion GT, Gates RD. From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS One 2012; 7:e38440. [PMID: 22701642 PMCID: PMC3368852 DOI: 10.1371/journal.pone.0038440] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 05/05/2012] [Indexed: 11/18/2022] Open
Abstract
Parental effects are ubiquitous in nature and in many organisms play a particularly critical role in the transfer of symbionts across generations; however, their influence and relative importance in the marine environment has rarely been considered. Coral reefs are biologically diverse and productive marine ecosystems, whose success is framed by symbiosis between reef-building corals and unicellular dinoflagellates in the genus Symbiodinium. Many corals produce aposymbiotic larvae that are infected by Symbiodinium from the environment (horizontal transmission), which allows for the acquisition of new endosymbionts (different from their parents) each generation. In the remaining species, Symbiodinium are transmitted directly from parent to offspring via eggs (vertical transmission), a mechanism that perpetuates the relationship between some or all of the Symbiodinium diversity found in the parent through multiple generations. Here we examine vertical transmission in the Hawaiian coral Montipora capitata by comparing the Symbiodinium ITS2 sequence assemblages in parent colonies and the eggs they produce. Parental effects on sequence assemblages in eggs are explored in the context of the coral genotype, colony morphology, and the environment of parent colonies. Our results indicate that ITS2 sequence assemblages in eggs are generally similar to their parents, and patterns in parental assemblages are different, and reflect environmental conditions, but not colony morphology or coral genotype. We conclude that eggs released by parent colonies during mass spawning events are seeded with different ITS2 sequence assemblages, which encompass phylogenetic variability that may have profound implications for the development, settlement and survival of coral offspring.
Collapse
|
8
|
Toonen RJ, Andrews KR, Baums IB, Bird CE, Concepcion GT, Daly-Engel TS, Eble JA, Faucci A, Gaither MR, Iacchei M, Puritz JB, Schultz JK, Skillings DJ, Timmers MA, Bowen BW. Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago. J Mar Biol 2011; 2011:460173. [PMID: 25505913 PMCID: PMC4260462 DOI: 10.1155/2011/460173] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions.
Collapse
Affiliation(s)
- Robert J. Toonen
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Kimberly R. Andrews
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Iliana B. Baums
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher E. Bird
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Gregory T. Concepcion
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Toby S. Daly-Engel
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jeff A. Eble
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Anuschka Faucci
- Department of Biology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Michelle R. Gaither
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Matthew Iacchei
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jonathan B. Puritz
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Jennifer K. Schultz
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| | - Derek J. Skillings
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
- Department of Zoology, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Molly A. Timmers
- Joint Institute for Marine and Atmospheric Research, University of Hawai’i at Mānoa, Honolulu, HI 96822, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawai’i at Mānoa, P.O. Box 1346 Kāne’ohe, HI 96744, USA
| |
Collapse
|
9
|
Gibbons TR, Concepcion GT, Bachvaroff TR, Delwiche CF. Evaluating short-read sequence data from the highly redundant, novel transcriptome of Polarella glacialis. Genome Biol 2011. [PMCID: PMC3439037 DOI: 10.1186/gb-2011-12-s1-p5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
10
|
Forsman ZH, Concepcion GT, Haverkort RD, Shaw RW, Maragos JE, Toonen RJ. Ecomorph or endangered coral? DNA and microstructure reveal hawaiian species complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli. PLoS One 2010; 5:e15021. [PMID: 21151995 PMCID: PMC2996308 DOI: 10.1371/journal.pone.0015021] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/24/2010] [Indexed: 11/17/2022] Open
Abstract
M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA), which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS) and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I) M. patula/M. verrilli, II) M. cf. incrassata, III) M. capitata, IV) M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA) of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA), two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity.
Collapse
Affiliation(s)
- Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, United States of America.
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
There is an ongoing debate on the scale of pelagic larval dispersal in promoting connectivity among populations of shallow, benthic marine organisms. The linearly arranged Hawaiian Islands are uniquely suited to study scales of population connectivity and have been used extensively as a natural laboratory in terrestrial systems. Here, we focus on Hawaiian populations of the lobe coral Porites lobata, an ecosystem engineer of shallow reefs throughout the Pacific. Patterns of recent gene flow and population structure in P. lobata samples (n = 318) from two regions, the Hawaiian Islands (n = 10 sites) and from their nearest neighbour Johnston Atoll, were analysed with nine microsatellite loci. Despite its massive growth form, ∼ 6% of the samples from both regions were the product of asexual reproduction via fragmentation. Cluster analysis and measures of genetic differentiation indicated that P. lobata from the Hawaiian Islands are strongly isolated from those on Johnston Atoll (F(ST) = 0.311; P < 0.001), with the descendants of recent migrants (n = 6) being clearly identifiable. Within the Hawaiian Islands, P. lobata conforms to a pattern of isolation by distance. Here, over 37% (P = 0.001) of the variation in genetic distance was explained by geographical distance. This pattern indicates that while the majority of ongoing gene flow in Hawaiian P. lobata occurs among geographically proximate reefs, inter-island distances are insufficient to generate strong population structure across the archipelago.
Collapse
Affiliation(s)
- Nicholas R Polato
- Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | | | | | | |
Collapse
|
12
|
Concepcion GT, Polato NR, Baums IB, Toonen RJ. Development of microsatellite markers from four Hawaiian corals: Acropora cytherea, Fungia scutaria, Montipora capitata and Porites lobata. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9118-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Chan YL, Pochon X, Fisher MA, Wagner D, Concepcion GT, Kahng SE, Toonen RJ, Gates RD. Generalist dinoflagellate endosymbionts and host genotype diversity detected from mesophotic (67-100 m depths) coral Leptoseris. BMC Ecol 2009; 9:21. [PMID: 19747389 PMCID: PMC2758838 DOI: 10.1186/1472-6785-9-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 09/11/2009] [Indexed: 11/17/2022] Open
Abstract
Background Mesophotic corals (light-dependent corals in the deepest half of the photic zone at depths of 30 - 150 m) provide a unique opportunity to study the limits of the interactions between corals and endosymbiotic dinoflagellates in the genus Symbiodinium. We sampled Leptoseris spp. in Hawaii via manned submersibles across a depth range of 67 - 100 m. Both the host and Symbiodinium communities were genotyped, using a non-coding region of the mitochondrial ND5 intron (NAD5) and the nuclear ribosomal internal transcribed spacer region 2 (ITS2), respectively. Results Coral colonies harbored endosymbiotic communities dominated by previously identified shallow water Symbiodinium ITS2 types (C1_ AF333515, C1c_ AY239364, C27_ AY239379, and C1b_ AY239363) and exhibited genetic variability at mitochondrial NAD5. Conclusion This is one of the first studies to examine genetic diversity in corals and their endosymbiotic dinoflagellates sampled at the limits of the depth and light gradients for hermatypic corals. The results reveal that these corals associate with generalist endosymbiont types commonly found in shallow water corals and implies that the composition of the Symbiodinium community (based on ITS2) alone is not responsible for the dominance and broad depth distribution of Leptoseris spp. The level of genetic diversity detected in the coral NAD5 suggests that there is undescribed taxonomic diversity in the genus Leptoseris from Hawaii.
Collapse
Affiliation(s)
- Yvonne L Chan
- Hawaii Institute of Marine Biology, PO Box 1346, Kaneohe, HI, 96744, USA.
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Bachvaroff TR, Concepcion GT, Rogers CR, Herman EM, Delwiche CF. Dinoflagellate Expressed Sequence Tag Data Indicate Massive Transfer of Chloroplast Genes to the Nuclear Genome. Protist 2004; 155:65-78. [PMID: 15144059 DOI: 10.1078/1434461000165] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The peridinin-pigmented plastids of dinoflagellates are very poorly understood, in part because of the paucity of molecular data available from these endosymbiotic organelles. To identify additional gene sequences that would carry information about the biology of the peridinin-type dinoflagellate plastid and its evolutionary history, an analysis was undertaken of arbitrarily selected sequences from cDNA libraries constructed from Lingulodinium polyedrum (1012 non-redundant sequences) and Amphidinium carterae (2143). Among the two libraries 118 unique plastid-associated sequences were identified, including 30 (most from A. carterae) that are encoded in the plastid genome of the red alga Porphyra. These sequences probably represent bona fide nuclear genes, and suggest that there has been massive transfer of genes from the plastid to the nuclear genome in dinoflagellates. These data support the hypothesis that the peridinin-type plastid has a minimal genome, and provide data that contradict the hypothesis that there is an unidentified canonical genome in the peridinin-type plastid. Sequences were also identified that were probably transferred directly from the nuclear genome of the red algal endosymbiont, as well as others that are distinctive to the Alveolata. A preliminary report of these data was presented at the Botany 2002 meeting in Madison, WI.
Collapse
Affiliation(s)
- Tsvetan R Bachvaroff
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | | | | | | | | |
Collapse
|