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Ditter RE, Campos M, Crepeau MW, Pinto J, Toilibou A, Amina Y, Tantely LM, Girod R, Lee Y, Cornel AJ, Lanzaro GC. Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations. Sci Rep 2023; 13:20830. [PMID: 38012255 PMCID: PMC10682471 DOI: 10.1038/s41598-023-44501-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/09/2023] [Indexed: 11/29/2023] Open
Abstract
The mosquito Anopheles gambiae s.s. is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern Africa. Previous studies have shown a relatively high degree of genetic isolation between the Comoros islands and mainland populations of A. gambiae, but the origin of the island populations remains unclear. Here, we analyzed phylogenetic relationships among island and mainland populations using complete mitochondrial genome sequences of individual A. gambiae specimens. This work augments earlier studies based on analysis of the nuclear genome. We investigated the source population of A. gambiae for each island, estimated the number of introductions, when they occurred and explored evidence for contemporary gene flow between island and mainland populations. These studies are relevant to understanding historical patterns in the dispersal of this important malaria vector and provide information critical to assessing their potential for the exploration of genetic-based vector control methods to eliminate this disease. Phylogenetic analysis and haplotype networks were constructed from mitogenome sequences of 258 A. gambiae from the four islands. In addition, 112 individuals from seven countries across sub-Saharan Africa and Madagascar were included to identify potential source populations. Our results suggest that introduction events of A. gambiae into the Comoros archipelago were rare and recent events and support earlier claims that gene flow between the mainland and these islands is limited. This study is concordant with earlier work suggesting the suitability of these oceanic islands as appropriate sites for conducting field trial releases of genetically engineered mosquitoes (GEMs).
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Affiliation(s)
- Robert E Ditter
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, UC Davis, 1089 Veterinary Medicine Dr, 4225 VM3B, Davis, CA, 95616, USA
| | - Melina Campos
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, UC Davis, 1089 Veterinary Medicine Dr, 4225 VM3B, Davis, CA, 95616, USA
| | - Marc W Crepeau
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, UC Davis, 1089 Veterinary Medicine Dr, 4225 VM3B, Davis, CA, 95616, USA
| | - João Pinto
- Global Health and Tropical Medicine, Instituto de Higiene E Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | | | | | - Luciano Michaël Tantely
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo 101, BP1274, Ambatofotsikely, Madagascar
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo 101, BP1274, Ambatofotsikely, Madagascar
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, 200 9th St SE, Vero Beach, FL, 32962, USA
| | - Anthony J Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, UC Davis, 1089 Veterinary Medicine Dr, 4225 VM3B, Davis, CA, 95616, USA
| | - Gregory C Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology and Immunology, UC Davis, 1089 Veterinary Medicine Dr, 4225 VM3B, Davis, CA, 95616, USA.
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Campos M, Patel N, Marshall C, Gripkey H, Ditter RE, Crepeau MW, Toilibou A, Amina Y, Cornel AJ, Lee Y, Lanzaro GC. Population Genetics of Anopheles pretoriensis in Grande Comore Island. Insects 2022; 14:14. [PMID: 36661943 PMCID: PMC9866569 DOI: 10.3390/insects14010014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Anopheles pretoriensis is widely distributed across Africa, including on oceanic islands such as Grande Comore in the Comoros. This species is known to be mostly zoophylic and therefore considered to have low impact on the transmission of human malaria. However, A. pretoriensis has been found infected with Plasmodium, suggesting that it may be epidemiologically important. In the present study, we sequenced and assembled the complete mitogenome of A. pretoriensis and inferred its phylogenetic relationship among other species in the subgenus Cellia. We also investigated the genetic structure of A. pretoriensis populations on Grande Comore Island, and between this island population and sites in continental Africa, using partial sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Seven haplotypes were found on the island, one of which was ubiquitous. There was no clear divergence between island haplotypes and those found on the continent. The present work contributes knowledge on this understudied, yet abundant, Anopheles species.
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Affiliation(s)
- Melina Campos
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | - Nikita Patel
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | - Carly Marshall
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | - Hans Gripkey
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | - Robert E. Ditter
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | - Marc W. Crepeau
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
| | | | | | - Anthony J. Cornel
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
- Mosquito Control Research Laboratory, Kearney Research and Extension Center, Department of Entomology and Nematology, University of California, Parlier, CA 93648, USA
| | - Yoosook Lee
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, 200 9th St SE, Vero Beach, FL 32962, USA
| | - Gregory C. Lanzaro
- Vector Genetics Laboratory, Department of Pathology, Microbiology, and Immunology, University of California, Davis, CA 95616, USA
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De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes (Basel) 2021; 12:110. [PMID: 33477542 PMCID: PMC7831106 DOI: 10.3390/genes12010110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Benjamin Wilhite
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Daniela Puiu
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - John Bradley St. Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA;
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Steven L. Salzberg
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Brian Allen
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
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Weiss M, Sniezko RA, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB, De La Torre AR. Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. Plant J 2020; 104:365-376. [PMID: 32654344 PMCID: PMC10773528 DOI: 10.1111/tpj.14928] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/17/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
The genomic architecture and molecular mechanisms controlling variation in quantitative disease resistance loci are not well understood in plant species and have been barely studied in long-generation trees. Quantitative trait loci mapping and genome-wide association studies were combined to test a large single nucleotide polymorphism (SNP) set for association with quantitative and qualitative white pine blister rust resistance in sugar pine. In the absence of a chromosome-scale reference genome, a high-density consensus linkage map was generated to obtain locations for associated SNPs. Newly discovered associations for white pine blister rust quantitative disease resistance included 453 SNPs involved in wide biological functions, including genes associated with disease resistance and others involved in morphological and developmental processes. In addition, NBS-LRR pathogen recognition genes were found to be involved in quantitative disease resistance, suggesting these newly reported genes are qualitative genes with partial resistance, they are the result of defeated qualitative resistance due to avirulent races, or they have epistatic effects on qualitative disease resistance genes. This study is a step forward in our understanding of the complex genomic architecture of quantitative disease resistance in long-generation trees, and constitutes the first step towards marker-assisted disease resistance breeding in white pine species.
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Affiliation(s)
- Matthew Weiss
- School of Forestry, Northern Arizona University, 200 E.
Pine Knoll, Flagstaff, AZ 86011
| | - Richard A. Sniezko
- Dorena Genetic Resource Center, USDA Forest Service,
Cottage-Grove, OR 97424
| | - Daniela Puiu
- Department of Biomedical Engineering, Computer Science and
Biostatistics and Center for Computational Biology, Johns Hopkins University, 3100
Wyman Park Dr., Wyman Park Building Room S220, Baltimore, MD 21211
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - Kristian Stevens
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - Steven L. Salzberg
- Department of Biomedical Engineering, Computer Science and
Biostatistics and Center for Computational Biology, Johns Hopkins University, 3100
Wyman Park Dr., Wyman Park Building Room S220, Baltimore, MD 21211
- Departments of Computer Science and Biostatistics, Johns
Hopkins University, Baltimore, MD 21218
| | - Charles H. Langley
- Department of Evolution and Ecology, University of
California-Davis, One Shields Avenue, Davis, CA 95616
| | - David B. Neale
- Department of Plant Sciences, University of
California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E.
Pine Knoll, Flagstaff, AZ 86011
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Marrano A, Martínez‐García PJ, Bianco L, Sideli GM, Di Pierro EA, Leslie CA, Stevens KA, Crepeau MW, Troggio M, Langley CH, Neale DB. A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density Axiom™ J. regia 700K SNP genotyping array. Plant Biotechnol J 2019; 17:1027-1036. [PMID: 30515952 PMCID: PMC6523593 DOI: 10.1111/pbi.13034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 07/30/2018] [Revised: 10/22/2018] [Accepted: 10/28/2018] [Indexed: 05/02/2023]
Abstract
Over the last 20 years, global production of Persian walnut (Juglans regia L.) has grown enormously, likely reflecting increased consumption due to its numerous benefits to human health. However, advances in genome-wide association (GWA) studies and genomic selection (GS) for agronomically important traits in walnut remain limited due to the lack of powerful genomic tools. Here, we present the development and validation of a high-density 700K single nucleotide polymorphism (SNP) array in Persian walnut. Over 609K high-quality SNPs have been thoroughly selected from a set of 9.6 m genome-wide variants, previously identified from the high-depth re-sequencing of 27 founders of the Walnut Improvement Program (WIP) of University of California, Davis. To validate the effectiveness of the array, we genotyped a collection of 1284 walnut trees, including 1167 progeny of 48 WIP families and 26 walnut cultivars. More than half of the SNPs (55.7%) fell in the highest quality class of 'Poly High Resolution' (PHR) polymorphisms, which were used to assess the WIP pedigree integrity. We identified 151 new parent-offspring relationships, all confirmed with the Mendelian inheritance test. In addition, we explored the genetic variability among cultivars of different origin, revealing how the varieties from Europe and California were differentiated from Asian accessions. Both the reconstruction of the WIP pedigree and population structure analysis confirmed the effectiveness of the Applied Biosystems™ Axiom™ J. regia 700K SNP array, which initiates a novel genomic and advanced phase in walnut genetics and breeding.
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Affiliation(s)
| | | | - Luca Bianco
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | - Gina M. Sideli
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Erica A. Di Pierro
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | | | | | - Marc W. Crepeau
- Department of Evolution and EcologyUniversity of CaliforniaDavisCAUSA
| | - Michela Troggio
- Research and Innovation CentreFondazione Edmund MachSan Michele all'AdigeTNItaly
| | | | - David B. Neale
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
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6
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Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC Genomics 2019; 20:331. [PMID: 31046664 PMCID: PMC6498479 DOI: 10.1186/s12864-019-5712-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus. Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Montanari
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Nahla V Bassil
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Joseph Postman
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Biff Kitson
- Motueka Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Motueka, New Zealand
| | - Cecilia H Deng
- Auckland Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kate Evans
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, USA
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De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB. Genomic architecture of complex traits in loblolly pine. New Phytol 2019; 221:1789-1801. [PMID: 30318590 DOI: 10.1111/nph.15535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 07/25/2018] [Accepted: 10/06/2018] [Indexed: 05/02/2023]
Abstract
Dissecting the genetic and genomic architecture of complex traits is essential to understand the forces maintaining the variation in phenotypic traits of ecological and economical importance. Whole-genome resequencing data were used to generate high-resolution polymorphic single nucleotide polymorphism (SNP) markers and genotype individuals from common gardens across the loblolly pine (Pinus taeda) natural range. Genome-wide associations were tested with a large phenotypic dataset comprising 409 variables including morphological traits (height, diameter, carbon isotope discrimination, pitch canker resistance), and molecular traits such as metabolites and expression of xylem development genes. Our study identified 2335 new SNP × trait associations for the species, with many SNPs located in physical clusters in the genome of the species; and the genomic location of hotspots for metabolic × genotype associations. We found a highly polygenic basis of quantitative inheritance, with significant differences in number, effects size, genomic location and frequency of alleles contributing to variation in phenotypes in the different traits. While mutation-selection balance might be shaping the genetic variation in metabolic traits, balancing selection is more likely to shape the variation in expression of xylem development genes. Our work contributes to the study of complex traits in nonmodel plant species by identifying associations at a whole-genome level.
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Affiliation(s)
- Amanda R De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Flagstaff, AZ, 86011, USA
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Daniela Puiu
- Center for Computational Biology, Johns Hopkins University, 1900 E. Monument St, Baltimore, MD, 21205, USA
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Kristian Stevens
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, 1900 E. Monument St, Baltimore, MD, 21205, USA
- Department of Biomedical Engineering, Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA, 95616, USA
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Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience 2017; 6:1. [PMID: 29020755 PMCID: PMC5632297 DOI: 10.1093/gigascience/gix072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.
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9
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Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience 2017; 6:1-4. [PMID: 28369353 PMCID: PMC5437942 DOI: 10.1093/gigascience/giw016] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022] Open
Abstract
The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly.
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Affiliation(s)
- Aleksey V Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, MD.,Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, CA
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT
| | - James A Yorke
- Institute for Physical Sciences and Technology, University of Maryland, College Park, MD
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD.,Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD
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Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. Plant J 2016; 87:507-32. [PMID: 27145194 DOI: 10.1111/tpj.13207] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [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: 09/21/2015] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 05/18/2023]
Abstract
The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.
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Affiliation(s)
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Jeanne Whalen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Robin Paul
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | | | - Russell L Reagan
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sriema L Walawage
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Charis Cardeno
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kevin Pratt
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Sowmya Kuruganti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JFD, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol 2014; 15:R59. [PMID: 24647006 PMCID: PMC4053751 DOI: 10.1186/gb-2014-15-3-r59] [Citation(s) in RCA: 274] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
Background The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. Results We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. Conclusions In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.
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Szabo Z, Crepeau MW, Mitchell AL, Stephan MJ, Puntel RA, Yin Loke K, Kirk RC, Urban Z. Aortic aneurysmal disease and cutis laxa caused by defects in the elastin gene. J Med Genet 2005; 43:255-8. [PMID: 16085695 PMCID: PMC2563239 DOI: 10.1136/jmg.2005.034157] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Cutis laxa is an acquired or inherited condition characterized by redundant, pendulous and inelastic skin. Autosomal dominant cutis laxa has been described as a benign disease with minor systemic involvement. OBJECTIVE To report a family with autosomal dominant cutis laxa and a young girl with sporadic cutis laxa, both with variable expression of an aortic aneurysmal phenotype ranging from mild dilatation to severe aneurysm or aortic rupture. METHODS AND RESULTS Histological evaluation of aortic aneurysmal specimens indicated classical hallmarks of medial degeneration, paucity of elastic fibres, and an absence of inflammatory or atherosclerotic lesions. Electron microscopy showed extracellular elastin deposits lacking microfibrillar elements. Direct sequencing of genomic amplimers detected defects in exon 30 of the elastin gene in affected individuals, but did not in 121 normal controls. The expression of mutant elastin mRNA forms was demonstrated by reverse transcriptase polymerase chain reaction analysis of cutis laxa fibroblasts. These mRNAs coded for multiple mutant tropoelastins, including C-terminally truncated and extended forms as well as for molecules lacking the constitutive exon 30. CONCLUSIONS ELN mutations may cause severe aortic disease in patients with cutis laxa. Thus regular cardiac monitoring is necessary in this disease to avert fatal aortic rupture.
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Abstract
Commercial sugarcane hybrid cultivars currently in production are high-yielding, disease-resistant, millable canes and are the result of years of breeding work. In Hawaii, these commercial hybrids are quite distinct from many Saccharum officinarum canes still in existence that were brought to the islands and cultivated by the native Polynesians. The actual genetic relationships among the native canes and the extent to which they contributed to the commercial hybrid germplasm has been the subject of speculation over the years. Genetic analysis of 43 presumed native Hawaiian S. officinarum clones using 228 DNA markers confirmed them to be a group distinct from the modern hybrid cultivars. The resulting dendrogram tended to confirm that there were several separate S. officinarum introductions that, owing to selections of somatic mutations, diverged into a number of cluster groups. When the "Sandwich Isles" were discovered by Captain James Cook in 1778, the Hawaiians were found to be growing sugarcane, S. officinarum ( Cook 1785). Sugarcane (ko, in the Hawaiian language) appeared in a variety of stalk and leaf colors, often with stripes (the "ribbon canes"). In the interest of preserving this historic germplasm, a collection was assembled in the 1920s by Edward L. Caum of the Hawaiian Sugar Planters' Association and W. W. G. Moir of American Factors. Histories and descriptions of the canes were reported by Moir (1932).
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Affiliation(s)
- S Schenck
- Hawaii Agriculture Research Center, 99-193 Aiea Heights Dr., Aiea, HI 96701, USA.
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Montgomery BL, Franklin KA, Terry MJ, Thomas B, Jackson SD, Crepeau MW, Lagarias JC. Biliverdin reductase-induced phytochrome chromophore deficiency in transgenic tobacco. Plant Physiol 2001; 125:266-77. [PMID: 11154335 PMCID: PMC61008 DOI: 10.1104/pp.125.1.266] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2000] [Revised: 08/03/2000] [Accepted: 09/05/2000] [Indexed: 05/21/2023]
Abstract
Targeted expression of mammalian biliverdin IXalpha reductase (BVR), an enzyme that metabolically inactivates linear tetrapyrrole precursors of the phytochrome chromophore, was used to examine the physiological functions of phytochromes in the qualitative short-day tobacco (Nicotiana tabacum cv Maryland Mammoth) plant. Comparative phenotypic and photobiological analyses of plastid- and cytosol-targeted BVR lines showed that multiple phytochrome-regulated processes, such as hypocotyl and internode elongation, anthocyanin synthesis, and photoperiodic regulation of flowering, were altered in all lines examined. The phytochrome-mediated processes of carotenoid and chlorophyll accumulation were strongly impaired in plastid-targeted lines, but were relatively unaffected in cytosol-targeted lines. Under certain growth conditions, plastid-targeted BVR expression was found to nearly abolish the qualitative inhibition of flowering by long-day photoperiods. The distinct phenotypes of the plastid-targeted BVR lines implicate a regulatory role for bilins in plastid development or, alternatively, reflect the consequence of altered tetrapyrrole metabolism in plastids due to bilin depletion.
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Affiliation(s)
- B L Montgomery
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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15
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Montgomery BL, Yeh KC, Crepeau MW, Lagarias JC. Modification of distinct aspects of photomorphogenesis via targeted expression of mammalian biliverdin reductase in transgenic Arabidopsis plants. Plant Physiol 1999; 121:629-39. [PMID: 10517855 PMCID: PMC59426 DOI: 10.1104/pp.121.2.629] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The phenotypic consequences of targeted expression of mammalian biliverdin IXalpha reductase (BVR), an enzyme that metabolically inactivates the linear tetrapyrrole precursors of the phytochrome chromophore, are addressed in this investigation. Through comparative phenotypic analyses of multiple plastid-targeted and cytosolic BVR transgenic Arabidopsis plant lines, we show that the subcellular localization of BVR affects distinct subsets of light-mediated and light-independent processes in plant growth and development. Regardless of its cellular localization, BVR suppresses the phytochrome-modulated responses of hypocotyl growth inhibition, sucrose-stimulated anthocyanin accumulation, and inhibition of floral initiation. By contrast, reduced protochlorophyll levels in dark-grown seedlings and fluence-rate-dependent reduction of chlorophyll occur only in transgenic plants in which BVR is targeted to plastids. Together with companion analyses of the phytochrome chromophore-deficient hy1 mutant, our results suggest a regulatory role for linear tetrapyrroles within the plastid compartment distinct from their assembly with apophytochromes in the cytosol.
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Affiliation(s)
- B L Montgomery
- Section of Molecular and Cellular Biology, One Shields Avenue, University of California, Davis, California 95616, USA
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Lagarias DM, Crepeau MW, Maines MD, Lagarias JC. Regulation of photomorphogenesis by expression of mammalian biliverdin reductase in transgenic Arabidopsis plants. Plant Cell 1997. [PMID: 9165746 DOI: 10.2307/3870424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The photoregulatory activity of the phytochrome photoreceptor requires the synthesis and covalent attachment of the linear tetrapyrrole prosthetic group phytochromobilin. Because the mammalian enzyme biliverdin IX alpha reductase (BVR) is able to functionally inactivate phytochromobilin in vitro, this investigation was undertaken to determine whether BVR expression in transgenic plants would prevent the synthesis of functionally active phytochrome in vivo. Here, we show that plastid-targeted, constitutive expression of BVR in Arabidopsis yields plants that display aberrant photomorphogenesis throughout their life cycle. Photobiological and biochemical analyses of three transgenic BVR lines exhibiting a 25-fold range of BVR expression established that the BVR-dependent phenotypes are light dependent, pleiotropic, and consonant with the loss of multiple phytochrome activities. Chlorophyll accumulation in BVR-expressing transgenic plants was particularly sensitive to increased light fluence rates, which is consistent with an important role for phytochrome in light tolerance. Under blue light, transgenic BVR plants displayed elongated hypocotyls but retained phototropic behavior and the ability to fully deetiolate. Directed BVR expression may prove to be useful for probing the cellular and developmental basis of phytochrome-mediated responses and for selective control of individual aspects of light-mediated plant growth and development.
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Affiliation(s)
- D M Lagarias
- Section of Molecular and Cellular Biology, University of California-Davis 95616, USA
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Lagarias DM, Crepeau MW, Maines MD, Lagarias JC. Regulation of photomorphogenesis by expression of mammalian biliverdin reductase in transgenic Arabidopsis plants. Plant Cell 1997; 9:675-88. [PMID: 9165746 PMCID: PMC156948 DOI: 10.1105/tpc.9.5.675] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The photoregulatory activity of the phytochrome photoreceptor requires the synthesis and covalent attachment of the linear tetrapyrrole prosthetic group phytochromobilin. Because the mammalian enzyme biliverdin IX alpha reductase (BVR) is able to functionally inactivate phytochromobilin in vitro, this investigation was undertaken to determine whether BVR expression in transgenic plants would prevent the synthesis of functionally active phytochrome in vivo. Here, we show that plastid-targeted, constitutive expression of BVR in Arabidopsis yields plants that display aberrant photomorphogenesis throughout their life cycle. Photobiological and biochemical analyses of three transgenic BVR lines exhibiting a 25-fold range of BVR expression established that the BVR-dependent phenotypes are light dependent, pleiotropic, and consonant with the loss of multiple phytochrome activities. Chlorophyll accumulation in BVR-expressing transgenic plants was particularly sensitive to increased light fluence rates, which is consistent with an important role for phytochrome in light tolerance. Under blue light, transgenic BVR plants displayed elongated hypocotyls but retained phototropic behavior and the ability to fully deetiolate. Directed BVR expression may prove to be useful for probing the cellular and developmental basis of phytochrome-mediated responses and for selective control of individual aspects of light-mediated plant growth and development.
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Affiliation(s)
- D M Lagarias
- Section of Molecular and Cellular Biology, University of California-Davis 95616, USA
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