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Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, Salzberg SL. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (Bethesda) 2022; 12:6460957. [PMID: 35100403 PMCID: PMC8728005 DOI: 10.1093/g3journal/jkab380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Alison D Scott
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Zane J Moore
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Emily Burns
- Save the Redwoods League, San Francisco, CA 94104, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
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Simler AB, Metz MR, Frangioso KM, Meentemeyer RK, Rizzo DM. Novel disturbance interactions between fire and an emerging disease impact survival and growth of resprouting trees. Ecology 2018; 99:2217-2229. [PMID: 30129261 DOI: 10.1002/ecy.2493] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 07/17/2018] [Indexed: 11/11/2022]
Abstract
Human-altered ecological disturbances may challenge system resilience and disrupt biological legacies maintaining ecosystem recovery. Yet, the extent to which novel regimes challenge these legacies varies. This may be partially explained by differences in the vulnerability of life history strategies to disturbance characteristics. In the fire-prone, resprouter-dominated coast redwood forests of California, the introduced disease sudden oak death (SOD) alters fuel profiles, fire behavior, and aboveground tree mortality; however, this system is dominated by resprouting trees that are well-adapted to aboveground damage, and belowground survival of individuals may represent the principal biological legacy connecting pre- and post-fire communities. Much of the research exploring altered disturbances and forest recovery has focused on legacies determined by seed dispersal and aboveground survival of adults. In this work, we use pre- and post-fire data from a long-term monitoring network to assess the impacts of novel disturbance interactions between wildfire and SOD on the belowground survival and vegetative reproduction of resprouters. We found that increasing accumulation of coarse woody surface fuels from SOD-killed hosts decreased the likelihood of belowground survival for resprouting tanoak trees, but not for redwoods. Tanoaks' belowground survival was negatively related to substrate burn severity, which increased with the volume of surface fuels from hosts, suggesting heat damage as a possible mechanism influencing altered patterns of resprouter mortality. These impacts increased with decreasing tree size. By contrast, redwood and tanoak trees that survived both disturbances resprouted more vigorously, regardless of post-fire infection by P. ramorum, and generated similar recruitment at the stand level. Our results demonstrate that disease-fire interactions can narrow recruitment filters for resprouters, which could impact long-term population and demographic structure; yet, compounded disturbance may also reduce stand density and disease pressure, allowing competitive release of survivors. Resprouters displayed vulnerabilities to altered disturbance, but our research suggests that legacies maintained by resprouting may be more resilient to certain compounded disturbances, compared to seed-obligate species, because of high rates of individual survival under increasingly severe events. These trends have important implications for conservation of declining tree species in SOD-impacted forests, as well as predictions of human impacts in other disturbance-prone systems where resprouters are present.
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Affiliation(s)
- Allison B Simler
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Margaret R Metz
- Department of Biology, Lewis & Clark College, Portland, Oregon, 97219, USA
| | - Kerri M Frangioso
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Ross K Meentemeyer
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Geospatial Analytics, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
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Harrison JG, Forister ML, Parchman TL, Koch GW. Vertical stratification of the foliar fungal community in the world's tallest trees. Am J Bot 2016; 103:2087-2095. [PMID: 27965238 DOI: 10.3732/ajb.1600277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/14/2016] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY The aboveground tissues of plants host numerous, ecologically important fungi, yet patterns in the spatial distribution of these fungi remain little known. Forest canopies in particular are vast reservoirs of fungal diversity, but intracrown variation in fungal communities has rarely been explored. Knowledge of how fungi are distributed throughout tree crowns will contribute to our understanding of interactions between fungi and their host trees and is a first step toward investigating drivers of community assembly for plant-associated fungi. Here we describe spatial patterns in fungal diversity within crowns of the world's tallest trees, coast redwoods (Sequoia sempervirens). METHODS We took a culture-independent approach, using the Illumina MiSeq platform, to characterize the fungal assemblage at multiple heights within the crown across the geographical range of the coast redwood. KEY RESULTS Within each tree surveyed, we uncovered evidence for vertical stratification in the fungal community; different portions of the tree crown harbored different assemblages of fungi. We also report between-tree variation in the fungal community within redwoods. CONCLUSIONS Our results suggest the potential for vertical stratification of fungal communities in the crowns of other tall tree species and should prompt future study of the factors giving rise to this stratification.
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Affiliation(s)
- Joshua G Harrison
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
- Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
| | - Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
- Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution, and Conservation Biology, Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
- Department of Biology, University of Nevada, Reno, 1664 North Virginia St., Nevada, USA
| | - George W Koch
- Department of Biological Sciences, Northern Arizona University, 617 S. Beaver St., Flagstaff, Arizona, USA
- Center for Ecosystem Science and Society, Northern Arizona University, P.O. Box 5620, Flagstaff, Arizona, USA
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Narayan L, Dodd RS, O’Hara KL. A genotyping protocol for multiple tissue types from the polyploid tree species Sequoia sempervirens (Cupressaceae). Appl Plant Sci 2015; 3:apps1400110. [PMID: 25798341 PMCID: PMC4356318 DOI: 10.3732/apps.1400110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). METHODS Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. RESULTS Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genetic distances on average. DISCUSSION The methods described in this paper will allow for the accurate identification of coast redwood clones, facilitating future studies of the reproductive ecology of this species. The techniques used in this paper can be applied to studies of other clonal organisms as well.
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Affiliation(s)
- Lakshmi Narayan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720-3114 USA
| | - Richard S. Dodd
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720-3114 USA
| | - Kevin L. O’Hara
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, California 94720-3114 USA
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