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Liu JJ, Sniezko R, Murray M, Wang N, Chen H, Zamany A, Sturrock RN, Savin D, Kegley A. Genetic Diversity and Population Structure of Whitebark Pine (Pinus albicaulis Engelm.) in Western North America. PLoS One 2016; 11:e0167986. [PMID: 27992468 PMCID: PMC5161329 DOI: 10.1371/journal.pone.0167986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/23/2016] [Indexed: 11/18/2022] Open
Abstract
Whitebark pine (WBP, Pinus albicaulis Engelm.) is an endangered conifer species due to heavy mortality from white pine blister rust (WPBR, caused by Cronartium ribicola) and mountain pine beetle (Dendroctonus ponderosae). Information about genetic diversity and population structure is of fundamental importance for its conservation and restoration. However, current knowledge on the genetic constitution and genomic variation is still limited for WBP. In this study, an integrated genomics approach was applied to characterize seed collections from WBP breeding programs in western North America. RNA-seq analysis was used for de novo assembly of the WBP needle transcriptome, which contains 97,447 protein-coding transcripts. Within the transcriptome, single nucleotide polymorphisms (SNPs) were discovered, and more than 22,000 of them were non-synonymous SNPs (ns-SNPs). Following the annotation of genes with ns-SNPs, 216 ns-SNPs within candidate genes with putative functions in disease resistance and plant defense were selected to design SNP arrays for high-throughput genotyping. Among these SNP loci, 71 were highly polymorphic, with sufficient variation to identify a unique genotype for each of the 371 individuals originating from British Columbia (Canada), Oregon and Washington (USA). A clear genetic differentiation was evident among seed families. Analyses of genetic spatial patterns revealed varying degrees of diversity and the existence of several genetic subgroups in the WBP breeding populations. Genetic components were associated with geographic variables and phenotypic rating of WPBR disease severity across landscapes, which may facilitate further identification of WBP genotypes and gene alleles contributing to local adaptation and quantitative resistance to WPBR. The WBP genomic resources developed here provide an invaluable tool for further studies and for exploitation and utilization of the genetic diversity preserved within this endangered conifer and other five-needle pines.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada
- * E-mail:
| | - Richard Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America
| | - Michael Murray
- Ministry of Forests, Lands and Natural Resource Operations, Nelson, BC, Canada
| | - Ning Wang
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada
- Qinghai University, Academy of Agriculture and Forestry Science, 253 Ningda Road, Xining, Qinghai, China
| | - Hao Chen
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada
| | - Arezoo Zamany
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada
| | - Rona N. Sturrock
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, Canada
| | - Douglas Savin
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America
| | - Angelia Kegley
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, United States of America
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202
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Gonzalez-Ibeas D, Martinez-Garcia PJ, Famula RA, Delfino-Mix A, Stevens KA, Loopstra CA, Langley CH, Neale DB, Wegrzyn JL. Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3 (BETHESDA, MD.) 2016; 6:3787-3802. [PMID: 27799338 PMCID: PMC5144951 DOI: 10.1534/g3.116.032805] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/13/2016] [Indexed: 02/06/2023]
Abstract
Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
| | | | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Annette Delfino-Mix
- United States Department of Agriculture Forest Service, Institute of Forest Genetics, Placerville, California 95667
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas 77843
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut 06269
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203
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Little SA, Boyes IG, Donaleshen K, von Aderkas P, Ehlting J. A transcriptomic resource for Douglas-fir seed development and analysis of transcription during late megagametophyte development. PLANT REPRODUCTION 2016; 29:273-286. [PMID: 27699505 DOI: 10.1007/s00497-016-0291-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/16/2016] [Indexed: 05/08/2023]
Abstract
Douglas-fir transcriptomics. Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) is economically important with extensive breeding programs and seed trade. However, the molecular genetics of its seed development are largely unknown. We developed a transcriptome resource covering key developmental stages of megagametophytes over time: prefertilization, fertilization, embryogenesis, and early, unfertilized abortion. RNA sequencing reads were assembled de novo into 105,505 predicted high-confidence transcripts derived from 34,521 predicted genes. Expression levels were estimated based on alignment of the original reads to the reference. Megagametophytes express a distinct set of genes compared to those of vegetative tissues. Transcripts related to signaling, protein turnover, and RNA biogenesis have lower expression values in vegetative tissues, whereas cell wall remodeling, solute transport, and seed storage protein transcripts have higher expression values in megagametophytes. Seed storage protein transcripts become very abundant in both pollinated and unpollinated megagametophytes over time, even in aborting ovules. However, the absence of protein storage bodies in unfertilized megagametophytes suggests extensive posttranscriptional mechanisms that either inhibit storage protein translation or their aggregation into protein bodies. This novel transcriptome resource provides a foundation for further important insights into conifer seed development.
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Affiliation(s)
- Stefan A Little
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
- Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Ian G Boyes
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Kate Donaleshen
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Patrick von Aderkas
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Jürgen Ehlting
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
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204
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Abstract
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.
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205
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Guan R, Zhao Y, Zhang H, Fan G, Liu X, Zhou W, Shi C, Wang J, Liu W, Liang X, Fu Y, Ma K, Zhao L, Zhang F, Lu Z, Lee SMY, Xu X, Wang J, Yang H, Fu C, Ge S, Chen W. Draft genome of the living fossil Ginkgo biloba. Gigascience 2016. [PMID: 27871309 DOI: 10.1186/s13742-016-0154-1pmid:27871309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. FINDINGS The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. CONCLUSIONS The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
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Affiliation(s)
- Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenbin Zhou
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | | | | | - Weiqing Liu
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | | | - Yuanyuan Fu
- BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | | | - Lijun Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | - Fumin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Chengxin Fu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China.
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Wenbin Chen
- BGI-Shenzhen, Shenzhen, 518083, China.
- BGI-Qingdao, Qingdao, 266555, China.
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206
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Guan R, Zhao Y, Zhang H, Fan G, Liu X, Zhou W, Shi C, Wang J, Liu W, Liang X, Fu Y, Ma K, Zhao L, Zhang F, Lu Z, Lee SMY, Xu X, Wang J, Yang H, Fu C, Ge S, Chen W. Draft genome of the living fossil Ginkgo biloba. Gigascience 2016; 5:49. [PMID: 27871309 PMCID: PMC5118899 DOI: 10.1186/s13742-016-0154-1] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies. However, the lack of a high-quality genome sequence has been an impediment to our understanding of its biology and evolution. FINDINGS The 10.61 Gb genome sequence containing 41,840 annotated genes was assembled in the present study. Repetitive sequences account for 76.58% of the assembled sequence, and long terminal repeat retrotransposons (LTR-RTs) are particularly prevalent. The diversity and abundance of LTR-RTs is due to their gradual accumulation and a remarkable amplification between 16 and 24 million years ago, and they contribute to the long introns and large genome. Whole genome duplication (WGD) may have occurred twice, with an ancient WGD consistent with that shown to occur in other seed plants, and a more recent event specific to ginkgo. Abundant gene clusters from tandem duplication were also evident, and enrichment of expanded gene families indicates a remarkable array of chemical and antibacterial defense pathways. CONCLUSIONS The ginkgo genome consists mainly of LTR-RTs resulting from ancient gradual accumulation and two WGD events. The multiple defense mechanisms underlying the characteristic resilience of ginkgo are fostered by a remarkable enrichment in ancient duplicated and ginkgo-specific gene clusters. The present study sheds light on sequencing large genomes, and opens an avenue for further genetic and evolutionary research.
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Affiliation(s)
- Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yunpeng Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenbin Zhou
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | | | | | - Weiqing Liu
- BGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China
| | | | - Yuanyuan Fu
- BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | | | - Lijun Zhao
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China
| | - Fumin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Chengxin Fu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, Institute of Ecology and Conservation Center for Gene Resources of Endangered Wildlife, Zhejiang University, Hangzhou, 310058, China.
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Wenbin Chen
- BGI-Shenzhen, Shenzhen, 518083, China.
- BGI-Qingdao, Qingdao, 266555, China.
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207
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Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ. Application of Genomic Technologies to the Breeding of Trees. Front Genet 2016; 7:198. [PMID: 27895664 PMCID: PMC5109026 DOI: 10.3389/fgene.2016.00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022] Open
Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
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Affiliation(s)
- Maria L Badenes
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - Angel Fernández I Martí
- Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain
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208
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Liu YY, Yang KZ, Wei XX, Wang XQ. Revisiting the phosphatidylethanolamine-binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. THE NEW PHYTOLOGIST 2016; 212:730-744. [PMID: 27375201 DOI: 10.1111/nph.14066] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/16/2016] [Indexed: 05/19/2023]
Abstract
Angiosperms and gymnosperms are two major groups of extant seed plants. It has been suggested that gymnosperms lack FLOWERING LOCUS T (FT), a key integrator at the core of flowering pathways in angiosperms. Taking advantage of newly released gymnosperm genomes, we revisited the evolutionary history of the plant phosphatidylethanolamine-binding protein (PEBP) gene family through phylogenetic reconstruction. Expression patterns in three gymnosperm taxa and heterologous expression in Arabidopsis were studied to investigate the functions of gymnosperm FT-like and TERMINAL FLOWER 1 (TFL1)-like genes. Phylogenetic reconstruction suggests that an ancient gene duplication predating the divergence of seed plants gave rise to the FT and TFL1 genes. Expression patterns indicate that gymnosperm TFL1-like genes play a role in the reproductive development process, while GymFT1 and GymFT2, the FT-like genes resulting from a duplication event in the common ancestor of gymnosperms, function in both growth rhythm and sexual development pathways. When expressed in Arabidopsis, both spruce FT-like and TFL1-like genes repressed flowering. Our study demonstrates that gymnosperms do have FT-like and TFL1-like genes. Frequent gene and genome duplications contributed significantly to the expansion of the plant PEBP gene family. The expression patterns of gymnosperm PEBP genes provide novel insight into the functional evolution of this gene family.
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Affiliation(s)
- Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Ke-Zhen Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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209
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Abstract
Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1 We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response.
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210
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Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
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211
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Moreno-Pachon NM, Leeggangers HACF, Nijveen H, Severing E, Hilhorst H, Immink RGH. Elucidating and mining the Tulipa and Lilium transcriptomes. PLANT MOLECULAR BIOLOGY 2016; 92:249-61. [PMID: 27387304 PMCID: PMC5566170 DOI: 10.1007/s11103-016-0508-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/27/2016] [Indexed: 05/03/2023]
Abstract
Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser ( http://www.bioinformatics.nl/bulbs/db/species/index ). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.
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Affiliation(s)
- Natalia M. Moreno-Pachon
- Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | | | - Harm Nijveen
- Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands
- Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands
| | - Edouard Severing
- Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Henk Hilhorst
- Wageningen Seed Laboratory (WSL), Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Richard G. H. Immink
- Physiology of Flower Bulbs, Department of Plant Physiology, Wageningen University, Wageningen, Netherlands
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212
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Liu JJ, Schoettle AW, Sniezko RA, Sturrock RN, Zamany A, Williams H, Ha A, Chan D, Danchok B, Savin DP, Kegley A. Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping. BMC Genomics 2016; 17:753. [PMID: 27663193 PMCID: PMC5034428 DOI: 10.1186/s12864-016-3079-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 09/08/2016] [Indexed: 12/18/2022] Open
Abstract
Background Linkage of DNA markers with phenotypic traits provides essential information to dissect clustered genes with potential phenotypic contributions in a target genome region. Pinus flexilis E. James (limber pine) is a keystone five-needle pine species in mountain-top ecosystems of North America. White pine blister rust (WPBR), caused by a non-native fungal pathogen Cronartium ribicola (J.C. Fisch.), has resulted in mortality in this conifer species and is still spreading through the distribution. The objective of this research was to develop P. flexilis transcriptome-wide single nucleotide polymorphism (SNP) markers using RNA-seq analysis for genetic mapping of the major gene (Cr4) that confers complete resistance to C. ribicola. Results Needle tissues of one resistant and two susceptible seedling families were subjected to RNA-seq analysis. In silico SNP markers were uncovered by mapping the RNA-seq reads back to the de novo assembled transcriptomes. A total of 110,573 in silico SNPs and 2,870 indels were identified with an average of 3.7 SNPs per Kb. These SNPs were distributed in 17,041 unigenes. Of these polymorphic P. flexilis unigenes, 6,584 were highly conserved as compared to the genome sequence of P. taeda L (loblolly pine). High-throughput genotyping arrays were designed and were used to search for Cr4-linked genic SNPs in megagametophyte populations of four maternal trees by haploid-segregation analysis. A total of 32 SNP markers in 25 genes were localized on the Cr4 linkage group (LG). Syntenic relationships of this Cr4-LG map with the model conifer species P. taeda anchored Cr4 on Pinus consensus LG8, indicating that R genes against C. ribicola have evolved independently in different five-needle pines. Functional genes close to Cr4 were annotated and their potential roles in Cr4-mediated resistance were further discussed. Conclusions We demonstrated a very effective, low-cost strategy for developing a SNP genetic map of a phenotypic trait of interest. SNP discovery through transcriptome comparison was integrated with high-throughput genotyping of a small set of in silico SNPs. This strategy may be applied to mapping any trait in non-model plant species that have complex genomes. Whole transcriptome sequencing provides a powerful tool for SNP discovery in conifers and other species with complex genomes, for which sequencing and annotation of complex genomes is still challenging. The genic SNP map for the consensus Cr4-LG may help future molecular breeding efforts by enabling both Cr4 positional characterization and selection of this gene against WPBR. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3079-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Jun Liu
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada.
| | - Anna W Schoettle
- USDA Forest Service, Rocky Mountain Research Station, 240 West Prospect Road, Fort Collins, CO, 80526, USA
| | - Richard A Sniezko
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
| | - Rona N Sturrock
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada
| | - Arezoo Zamany
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada
| | - Holly Williams
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada
| | - Amanda Ha
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada
| | - Danelle Chan
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC, V8Z 1 M5, Canada
| | - Bob Danchok
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
| | - Douglas P Savin
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
| | - Angelia Kegley
- USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR, 97424, USA
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213
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Yeaman S, Hodgins KA, Lotterhos KE, Suren H, Nadeau S, Degner JC, Nurkowski KA, Smets P, Wang T, Gray LK, Liepe KJ, Hamann A, Holliday JA, Whitlock MC, Rieseberg LH, Aitken SN. Convergent local adaptation to climate in distantly related conifers. Science 2016; 353:1431-1433. [DOI: 10.1126/science.aaf7812] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023]
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Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics 2016; 17:730. [PMID: 27624183 PMCID: PMC5022155 DOI: 10.1186/s12864-016-3081-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, 37077, Germany. .,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, 119333, Russia. .,Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, 23332 Success Road, Saucier, MS, 39574, USA.,University of Kentucky, Forest Health Research and Education Center, 730 Rose Street, Lexington, KY, 40546, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA
| | - Thomas D Byram
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Texas A&M Forest Service, 2585 TAMU, College Station, TX, 77843-2585, USA
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
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215
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Santos FC, Guyot R, do Valle CB, Chiari L, Techio VH, Heslop-Harrison P, Vanzela ALL. Chromosomal distribution and evolution of abundant retrotransposons in plants: gypsy elements in diploid and polyploid Brachiaria forage grasses. Chromosome Res 2016; 23:571-82. [PMID: 26386563 DOI: 10.1007/s10577-015-9492-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low-copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thousands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequences that amplify via an RNA intermediate and reinsert into the genome, are often the major fraction of a genome. Here, we put research on retrotransposons into the larger context of plant repetitive DNA and genome behaviour, showing features of genome evolution in a grass genus, Brachiaria, in relation to other plant species. We show the contrasting amplification of different retroelement fractions across the genome with characteristics for various families and domains. The genus Brachiaria includes both diploid and polyploid species, with similar chromosome types and chromosome basic numbers x = 6, 7, 8 and 9. The polyploids reproduce asexually and are apomictic, but there are also sexual species. Cytogenetic studies and flow cytometry indicate a large variation in DNA content (C-value), chromosome sizes and genome organization. In order to evaluate the role of transposable elements in the genome and karyotype organization of species of Brachiaria, we searched for sequences similar to conserved regions of TEs in RNAseq reads library produced in Brachiaria decumbens. Of the 9649 TE-like contigs, 4454 corresponded to LTR-retrotransposons, and of these, 79.5 % were similar to members of the gypsy superfamily. Sequences of conserved protein domains of gypsy were used to design primers for producing the probes. The probes were used in FISH against chromosomes of accesses of B. decumbens, Brachiaria brizantha, Brachiaria ruziziensis and Brachiaria humidicola. Probes showed hybridization signals predominantly in proximal regions, especially those for retrotransposons of the clades CRM and Athila, while elements of Del and Tat exhibited dispersed signals, in addition to those proximal signals. These results show that the proximal region of Brachiaria chromosomes is a hotspot for retrotransposon insertion, particularly for the gypsy family. The combination of high-throughput sequencing and a chromosome-centric cytogenetic approach allows the abundance, organization and nature of transposable elements to be characterized in unprecedented detail. By their amplification and dispersal, retrotransposons can affect gene expression; they can lead to rapid diversification of chromosomes between species and, hence, are useful for studies of genome evolution and speciation in the Brachiaria genus. Centromeric regions can be identified and mapped, and retrotransposon markers can also assisting breeders in the developing and exploiting interspecific hybrids.
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Affiliation(s)
- Fabíola Carvalho Santos
- Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina, 86057-970, Paraná State, Brazil
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR IPME, BP 64501, 34394, Montpellier Cedex, France
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, 79106-550, Campo Grande, Mato Grosso do Sul State, Brazil
| | - Vânia Helena Techio
- Department of Biology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais State, Brazil
| | | | - André Luís Laforga Vanzela
- Department of General Biology, Center of Biological Sciences, State University of Londrina, Londrina, 86057-970, Paraná State, Brazil.
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216
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Glenn TC, Faircloth BC. Capturing Darwin's dream. Mol Ecol Resour 2016; 16:1051-8. [PMID: 27454358 PMCID: PMC5318190 DOI: 10.1111/1755-0998.12574] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 01/28/2023]
Abstract
Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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217
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Savolainen O, Lascoux M. Geography matters for Arabidopsis. Nature 2016; 537:314-315. [DOI: 10.1038/nature19466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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218
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Nemesio-Gorriz M, Hammerbacher A, Ihrmark K, Källman T, Olson Å, Lascoux M, Stenlid J, Gershenzon J, Elfstrand M. Different Alleles of a Gene Encoding Leucoanthocyanidin Reductase (PaLAR3) Influence Resistance against the Fungus Heterobasidion parviporum in Picea abies. PLANT PHYSIOLOGY 2016; 171:2671-81. [PMID: 27317690 PMCID: PMC4972290 DOI: 10.1104/pp.16.00685] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/11/2016] [Indexed: 05/18/2023]
Abstract
Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.
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Affiliation(s)
- Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Almuth Hammerbacher
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Katarina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Thomas Källman
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Martin Lascoux
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Jonathan Gershenzon
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden (M.N.-G., K.I., A.O., J.S., M.E.);Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, 0002 Pretoria, South Africa (A.H.);Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden (T.K., M.L.);BILS, Science for Life Laboratory, 75237 Uppsala, Sweden (T.K.); and Department of Biochemistry, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany (J.G.)
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Jiang P, Nelson JD, Leng N, Collins M, Swanson S, Dewey CN, Thomson JA, Stewart R. Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Dev Biol 2016; 426:143-154. [PMID: 27475628 DOI: 10.1016/j.ydbio.2016.05.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 05/20/2016] [Accepted: 05/21/2016] [Indexed: 12/14/2022]
Abstract
The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9-11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and neurulation. These results yield new insights into global gene expression during early stages of amphibian embryogenesis and will help to further develop the axolotl as a model species for developmental and regenerative biology.
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Affiliation(s)
- Peng Jiang
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Jeffrey D Nelson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Ning Leng
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Michael Collins
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Scott Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States; Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, United States; Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, United States
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States.
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The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Sci Rep 2016; 6:30444. [PMID: 27457880 PMCID: PMC4960570 DOI: 10.1038/srep30444] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/30/2016] [Indexed: 12/14/2022] Open
Abstract
Basic leucine zippers (bZIPs) form a large plant transcription factor family. C and S1 bZIP groups can heterodimerize, fulfilling crucial roles in seed development and stress response. S1 sequences also harbor a unique regulatory mechanism, termed Sucrose-Induced Repression of Translation (SIRT). The conservation of both C/S1 bZIP interactions and SIRT remains poorly characterized in non-model species, leaving their evolutionary origin uncertain and limiting crop research. In this work, we explored recently published plant sequencing data to establish a detailed phylogeny of C and S1 bZIPs, investigating their intertwined role in plant evolution, and the origin of SIRT. Our analyses clarified C and S1 bZIP orthology relationships in angiosperms, and identified S1 sequences in gymnosperms. We experimentally showed that the gymnosperm orthologs are regulated by SIRT, tracing back the origin of this unique regulatory mechanism to the ancestor of seed plants. Additionally, we discovered an earlier S ortholog in the charophyte algae Klebsormidium flaccidum, together with a C ortholog. This suggests that C and S groups originated by duplication from a single algal proto-C/S ancestor. Based on our observations, we propose a model wherein the C/S1 bZIP dimer network evolved in seed plants from pre-existing C/S bZIP interactions.
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221
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Pascual MB, El-Azaz J, de la Torre FN, Cañas RA, Avila C, Cánovas FM. Biosynthesis and Metabolic Fate of Phenylalanine in Conifers. FRONTIERS IN PLANT SCIENCE 2016; 7:1030. [PMID: 27468292 PMCID: PMC4942462 DOI: 10.3389/fpls.2016.01030] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/18/2023]
Abstract
The amino acid phenylalanine (Phe) is a critical metabolic node that plays an essential role in the interconnection between primary and secondary metabolism in plants. Phe is used as a protein building block but it is also as a precursor for numerous plant compounds that are crucial for plant reproduction, growth, development, and defense against different types of stresses. The metabolism of Phe plays a central role in the channeling of carbon from photosynthesis to the biosynthesis of phenylpropanoids. The study of this metabolic pathway is particularly relevant in trees, which divert large amounts of carbon into the biosynthesis of Phe-derived compounds, particularly lignin, an important constituent of wood. The trunks of trees are metabolic sinks that consume a considerable percentage of carbon and energy from photosynthesis, and carbon is finally immobilized in wood. This paper reviews recent advances in the biosynthesis and metabolic utilization of Phe in conifer trees. Two alternative routes have been identified: the ancient phenylpyruvate pathway that is present in microorganisms, and the arogenate pathway that possibly evolved later during plant evolution. Additionally, an efficient nitrogen recycling mechanism is required to maintain sustained growth during xylem formation. The relevance of phenylalanine metabolic pathways in wood formation, the biotic interactions, and ultraviolet protection is discussed. The genetic manipulation and transcriptional regulation of the pathways are also outlined.
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Affiliation(s)
| | | | | | | | | | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de MálagaMálaga, Spain
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Mora-Márquez F, García-Olivares V, Emerson BC, López de Heredia U. ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments. Mol Ecol Resour 2016; 17:230-246. [DOI: 10.1111/1755-0998.12550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/11/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022]
Affiliation(s)
- F. Mora-Márquez
- Forest Genetics and Physiology Research Group; Technical University of Madrid (UPM); Ciudad Universitaria s/n Madrid Spain
| | - V. García-Olivares
- Island Ecology and Evolution Research Group; IPNA-CSIC; Tenerife Canary Islands Spain
| | - B. C. Emerson
- Island Ecology and Evolution Research Group; IPNA-CSIC; Tenerife Canary Islands Spain
- School of Biological Sciences; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - U. López de Heredia
- Forest Genetics and Physiology Research Group; Technical University of Madrid (UPM); Ciudad Universitaria s/n Madrid Spain
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223
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Lin X, Faridi N, Casola C. An Ancient Transkingdom Horizontal Transfer of Penelope-Like Retroelements from Arthropods to Conifers. Genome Biol Evol 2016; 8:1252-66. [PMID: 27190138 PMCID: PMC4860704 DOI: 10.1093/gbe/evw076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Comparative genomics analyses empowered by the wealth of sequenced genomes have revealed numerous instances of horizontal DNA transfers between distantly related species. In eukaryotes, repetitive DNA sequences known as transposable elements (TEs) are especially prone to move across species boundaries. Such horizontal transposon transfers, or HTTs, are relatively common within major eukaryotic kingdoms, including animals, plants, and fungi, while rarely occurring across these kingdoms. Here, we describe the first case of HTT from animals to plants, involving TEs known as Penelope-like elements, or PLEs, a group of retrotransposons closely related to eukaryotic telomerases. Using a combination of in situ hybridization on chromosomes, polymerase chain reaction experiments, and computational analyses we show that the predominant PLE lineage, EN(+)PLEs, is highly diversified in loblolly pine and other conifers, but appears to be absent in other gymnosperms. Phylogenetic analyses of both protein and DNA sequences reveal that conifers EN(+)PLEs, or Dryads, form a monophyletic group clustering within a clade of primarily arthropod elements. Additionally, no EN(+)PLEs were detected in 1,928 genome assemblies from 1,029 nonmetazoan and nonconifer genomes from 14 major eukaryotic lineages. These findings indicate that Dryads emerged following an ancient horizontal transfer of EN(+)PLEs from arthropods to a common ancestor of conifers approximately 340 Ma. This represents one of the oldest known interspecific transmissions of TEs, and the most conspicuous case of DNA transfer between animals and plants.
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Affiliation(s)
- Xuan Lin
- Department of Ecosystem Science and Management, Texas A&M University
| | - Nurul Faridi
- Department of Ecosystem Science and Management, Texas A&M University Southern Institute of Forest Genetics, USDA Forest Service Southern Research Station, Saucier, Mississippi
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
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Geisler K, Jensen NB, Yuen MMS, Madilao L, Bohlmann J. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products. PLANT PHYSIOLOGY 2016; 171:152-64. [PMID: 26936895 PMCID: PMC4854711 DOI: 10.1104/pp.16.00180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 05/06/2023]
Abstract
Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.
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Affiliation(s)
- Katrin Geisler
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Niels Berg Jensen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Lina Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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225
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Alegre S, Pascual J, Nagler M, Weckwerth W, Cañal MJ, Valledor L. Dataset of UV induced changes in nuclear proteome obtained by GeLC-Orbitrap/MS in Pinus radiata needles. Data Brief 2016; 7:1477-82. [PMID: 27182543 PMCID: PMC4857224 DOI: 10.1016/j.dib.2016.03.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 01/12/2023] Open
Abstract
Although responses to UV stress have been characterised at system and cellular levels, the dynamics of the nuclear proteome triggered in this situation are still unknown, despite its essential role in regulating gene expression and in last term plant physiology. To fill this gap, we characterised the variations in the nuclear proteome after 2 h and 16 h (8 h/day) of UV irradiation by using state-of-the-art mass spectrometry-based shotgun proteomics methods combined with novel bioinformatics workflows that were employed in the manuscript entitled "The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata" (Pascual et al., 2016) [1]. We employed in-gel digestion followed by a 120 min gradient prior to MS analysis. Data was processed following two approaches: a database dependent employing the SEQUEST algorithm and custom databases, and a database independent by mass accuracy precursor alignment (MAPA). 388 proteins were identified by SEQUEST search and 9094 m/z were quantified by MAPA. Significant m/z were de novo sequenced using the Novor algorithm. We present here the complete datasets and the analysis workflow.
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Affiliation(s)
- Sara Alegre
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Jesús Pascual
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Matthias Nagler
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - María Jesús Cañal
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
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226
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Lamara M, Raherison E, Lenz P, Beaulieu J, Bousquet J, MacKay J. Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce. THE NEW PHYTOLOGIST 2016; 210:240-55. [PMID: 26619072 PMCID: PMC5063130 DOI: 10.1111/nph.13762] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/13/2015] [Indexed: 05/02/2023]
Abstract
Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects. Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
| | - Elie Raherison
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
| | - Patrick Lenz
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canadian Wood Fibre CentreCanadian Forest ServiceNatural Resources CanadaQuébecQCG1V 4C7Canada
| | - Jean Beaulieu
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canadian Wood Fibre CentreCanadian Forest ServiceNatural Resources CanadaQuébecQCG1V 4C7Canada
- Canada Research Chair in Forest and Environmental GenomicsUniversité LavalQuébecQCG1V 0A6Canada
| | - Jean Bousquet
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Canada Research Chair in Forest and Environmental GenomicsUniversité LavalQuébecQCG1V 0A6Canada
| | - John MacKay
- Forest Research Centre, and Institute for System and Integrative BiologyUniversité LavalQuébecQCG1V 0A6Canada
- Department of Plant SciencesUniversity of OxfordOxford0X1 3RBUK
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227
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Kusch S, Pesch L, Panstruga R. Comprehensive Phylogenetic Analysis Sheds Light on the Diversity and Origin of the MLO Family of Integral Membrane Proteins. Genome Biol Evol 2016; 8:878-95. [PMID: 26893454 PMCID: PMC4824068 DOI: 10.1093/gbe/evw036] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 12/11/2022] Open
Abstract
Mildew resistanceLocusO(MLO) proteins are polytopic integral membrane proteins that have long been considered as plant-specific and being primarily involved in plant-powdery mildew interactions. However, research in the past decade has revealed that MLO proteins diverged into a family with several clades whose members are associated with different physiological processes. We provide a largely increased dataset of MLO amino acid sequences, comprising nearly all major land plant lineages. Based on this comprehensive dataset, we defined seven phylogenetic clades and reconstructed the likely evolution of the MLO family in embryophytes. We further identified several MLO peptide motifs that are either conserved in all MLO proteins or confined to one or several clades, supporting the notion that clade-specific diversification of MLO functions is associated with particular sequence motifs. In baker's yeast, some of these motifs are functionally linked to transmembrane (TM) transport of organic molecules and ions. In addition, we attempted to define the evolutionary origin of the MLO family and found that MLO-like proteins with highly diverse membrane topologies are present in green algae, but also in the distinctly related red algae (Rhodophyta), Amoebozoa, and Chromalveolata. Finally, we discovered several instances of putative fusion events between MLO proteins and different kinds of proteins. Such Rosetta stone-type hybrid proteins might be instructive for future analysis of potential MLO functions. Our findings suggest that MLO is an ancient protein that possibly evolved in unicellular photosynthetic eukaryotes, and consolidated in land plants with a conserved topology, comprising seven TM domains and an intrinsically unstructured C-terminus.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Lina Pesch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, 52056 Aachen, Germany
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228
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The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata. J Proteomics 2016; 143:390-400. [PMID: 26961940 DOI: 10.1016/j.jprot.2016.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 12/31/2022]
Abstract
UNLABELLED The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees. SIGNIFICANCE The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs.
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229
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Hu XG, Liu H, Jin Y, Sun YQ, Li Y, Zhao W, El-Kassaby YA, Wang XR, Mao JF. De Novo Transcriptome Assembly and Characterization for the Widespread and Stress-Tolerant Conifer Platycladus orientalis. PLoS One 2016; 11:e0148985. [PMID: 26881995 PMCID: PMC4755536 DOI: 10.1371/journal.pone.0148985] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 01/26/2016] [Indexed: 11/18/2022] Open
Abstract
Platycladus orientalis, of the family Cupressaceae, is a widespread conifer throughout China and is extensively used for ecological reforestation, horticulture, and in medicine. Transcriptome assemblies are required for this ecologically important conifer for understanding genes underpinning adaptation and complex traits for breeding programs. To enrich the species' genomic resources, a de novo transcriptome sequencing was performed using Illumina paired-end sequencing. In total, 104,073,506 high quality sequence reads (approximately 10.3 Gbp) were obtained, which were assembled into 228,948 transcripts and 148,867 unigenes that were longer than 200 nt. Quality assessment using CEGMA showed that the transcriptomes obtained were mostly complete for highly conserved core eukaryotic genes. Based on similarity searches with known proteins, 62,938 (42.28% of all unigenes), 42,158 (28.32%), and 23,179 (15.57%) had homologs in the Nr, GO, and KOG databases, 25,625 (17.21%) unigenes were mapped to 322 pathways by BLASTX comparison against the KEGG database and 1,941 unigenes involved in environmental signaling and stress response were identified. We also identified 43 putative terpene synthase (TPS) functional genes loci and compared them with TPSs from other species. Additionally, 5,296 simple sequence repeats (SSRs) were identified in 4,715 unigenes, which were assigned to 142 motif types. This is the first report of a complete transcriptome analysis of P. orientalis. These resources provide a foundation for further studies of adaptation mechanisms and molecular-based breeding programs.
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Affiliation(s)
- Xian-Ge Hu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hui Liu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - YuQing Jin
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yan-Qiang Sun
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yue Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wei Zhao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiao-Ru Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- * E-mail:
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230
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Wu H, Ma Z, Wang MM, Qin AL, Ran JH, Wang XQ. A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features. Mol Ecol 2016; 25:1192-210. [PMID: 26800145 PMCID: PMC7168403 DOI: 10.1111/mec.13538] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
The origin and evolution of polyploids have been studied extensively in angiosperms and ferns but very rarely in gymnosperms. With the exception of three species of conifers, all natural polyploid species of gymnosperms belong to Ephedra, in which more than half of the species show polyploid cytotypes. Here, we investigated the origin and evolution of polyploids of Ephedra distributed in the Qinghai–Tibetan Plateau (QTP) and neighbouring areas. Flow cytometry (FCM) was used to measure the ploidy levels of the sampled species that are represented by multiple individuals from different populations, and then, two single‐copy nuclear genes (LFY and DDB2) and two chloroplast DNA fragments were used to unravel the possible origins and maternal donors of the polyploids. The results indicate that the studied polyploid species are allopolyploids, and suggest that allotetraploidy is a dominant mode of speciation in Ephedra. The high percentage of polyploids in the genus could be related to some of its biological attributes such as vegetative propagation, a relatively high rate of unreduced gamete formation, and a small genome size relative to most other gymnosperms. Significant ecological divergences between allotetraploids and their putative progenitors were detected by PCAs and anova and Tukey's tests, with the exception of E. saxatilis. The overlap of geographical distributions and ecological niches of some diploid species could have provided opportunities for interspecific hybridization and allopolyploid speciation.
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Affiliation(s)
- Hui Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhen Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ming-Ming Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ai-Li Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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231
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Kanazawa T, Era A, Minamino N, Shikano Y, Fujimoto M, Uemura T, Nishihama R, Yamato KT, Ishizaki K, Nishiyama T, Kohchi T, Nakano A, Ueda T. SNARE Molecules in Marchantia polymorpha: Unique and Conserved Features of the Membrane Fusion Machinery. PLANT & CELL PHYSIOLOGY 2016; 57:307-24. [PMID: 26019268 DOI: 10.1093/pcp/pcv076] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/22/2015] [Indexed: 05/18/2023]
Abstract
The membrane trafficking pathway has been diversified in a specific way for each eukaryotic lineage, probably to fulfill specific functions in the organisms. In green plants, comparative genomics has supported the possibility that terrestrialization and/or multicellularization could be associated with the elaboration and diversification of membrane trafficking pathways, which have been accomplished by an expansion of the numbers of genes required for machinery components of membrane trafficking, including soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. However, information regarding membrane trafficking pathways in basal land plant lineages remains limited. In the present study, we conducted extensive analyses of SNARE molecules, which mediate membrane fusion between target membranes and transport vesicles or donor organelles, in the liverwort, Marchantia polymorpha. The M. polymorpha genome contained at least 34 genes for 36 SNARE proteins, comprising fundamental sets of SNARE proteins that are shared among land plant lineages with low degrees of redundancy. We examined the subcellular distribution of a major portion of these SNARE proteins by expressing Citrine-tagged SNARE proteins in M. polymorpha, and the results showed that some of the SNARE proteins were targeted to different compartments from their orthologous products in Arabidopsis thaliana. For example, MpSYP12B was localized to the surface of the oil body, which is a unique organelle in liverworts. Furthermore, we identified three VAMP72 members with distinctive structural characteristics, whose N-terminal extensions contain consensus sequences for N-myristoylation. These results suggest that M. polymorpha has acquired unique membrane trafficking pathways associated with newly acquired machinery components during evolution.
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Affiliation(s)
- Takehiko Kanazawa
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Atsuko Era
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Department of Cell Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
| | - Naoki Minamino
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yu Shikano
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Tomohiro Uemura
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kinki University, Nishimitani, Kinokawa, Wakayama, 649-6493 Japan
| | - Kimitsune Ishizaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Tomoaki Nishiyama
- Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-0934 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Akihiko Nakano
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Takashi Ueda
- Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
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Takuno S, Ran JH, Gaut BS. Evolutionary patterns of genic DNA methylation vary across land plants. NATURE PLANTS 2016; 2:15222. [PMID: 27249194 DOI: 10.1038/nplants.2015.222] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 12/18/2015] [Indexed: 05/18/2023]
Abstract
Little is known about patterns of genic DNA methylation across the plant kingdom or about the evolutionary processes that shape them. To characterize gene-body methylation (gbM) within exons, we have gathered single-base resolution methylome data that span the phylogenetic breadth of land plants. We find that a basal land plant, Marchantia polymorpha, lacks any evident signal of gbM within exons, but conifers have high levels of both CG and CHG (where H is A, C or T) methylation in expressed genes. To begin to understand the evolutionary forces that shape gbM, we first tested for correlations in methylation levels across orthologues(1,2). Genic CG methylation levels, but not CHG or CHH levels, are correlated across orthologues for species as distantly related as ferns and angiosperms. Hence, relative levels of CG methylation are a consistent property across genes, even for species that diverged ∼400 million years ago(3,4). In contrast, genic CHG methylation correlates with genome size, suggesting that the host epigenetic response to transposable elements also affects genes. Altogether, our data indicate that the evolutionary forces acting on DNA methylation vary substantially across species, genes and methylation contexts.
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Affiliation(s)
- Shohei Takuno
- SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa 240-0193, Japan
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, California 92697-2525, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, 321 Steinhaus Hall, Irvine, California 92697-2525, USA
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Koralewski TE, Mateos M, Krutovsky KV. Conflicting genomic signals affect phylogenetic inference in four species of North American pines. AOB PLANTS 2016; 8:plw019. [PMID: 27060161 PMCID: PMC4866652 DOI: 10.1093/aobpla/plw019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/19/2016] [Indexed: 05/14/2023]
Abstract
Adaptive evolutionary processes in plants may be accompanied by episodes of introgression, parallel evolution and incomplete lineage sorting that pose challenges in untangling species evolutionary history. Genus Pinus (pines) is one of the most abundant and most studied groups among gymnosperms, and a good example of a lineage where these phenomena have been observed. Pines are among the most ecologically and economically important plant species. Some, such as the pines of the southeastern USA (southern pines in subsection Australes), are subjects of intensive breeding programmes. Despite numerous published studies, the evolutionary history of Australes remains ambiguous and often controversial. We studied the phylogeny of four major southern pine species: shortleaf (Pinus echinata), slash (P. elliottii), longleaf (P. palustris) and loblolly (P. taeda), using sequences from 11 nuclear loci and maximum likelihood and Bayesian methods. Our analysis encountered resolution difficulties similar to earlier published studies. Although incomplete lineage sorting and introgression are two phenomena presumptively underlying our results, the phylogenetic inferences seem to be also influenced by the genes examined, with certain topologies supported by sets of genes sharing common putative functionalities. For example, genes involved in wood formation supported the clade echinata-taeda, genes linked to plant defence supported the clade echinata-elliottii and genes linked to water management properties supported the clade echinata-palustris The support for these clades was very high and consistent across methods. We discuss the potential factors that could underlie these observations, including incomplete lineage sorting, hybridization and parallel or adaptive evolution. Our results likely reflect the relatively short evolutionary history of the subsection that is thought to have begun during the middle Miocene and has been influenced by climate fluctuations.
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Affiliation(s)
- Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 2258 TAMU, College Station, TX 77843-2258, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, USA Department of Forest Genetics and Forest Tree Breeding, Büsgen-Institute, Georg-August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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Abstract
The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://www.plantontology.org/ ) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.
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235
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Isik F, Bartholomé J, Farjat A, Chancerel E, Raffin A, Sanchez L, Plomion C, Bouffier L. Genomic selection in maritime pine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:108-119. [PMID: 26566829 DOI: 10.1016/j.plantsci.2015.08.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 05/05/2023]
Abstract
A two-generation maritime pine (Pinus pinaster Ait.) breeding population (n=661) was genotyped using 2500 SNP markers. The extent of linkage disequilibrium and utility of genomic selection for growth and stem straightness improvement were investigated. The overall intra-chromosomal linkage disequilibrium was r(2)=0.01. Linkage disequilibrium corrected for genomic relationships derived from markers was smaller (rV(2)=0.006). Genomic BLUP, Bayesian ridge regression and Bayesian LASSO regression statistical models were used to obtain genomic estimated breeding values. Two validation methods (random sampling 50% of the population and 10% of the progeny generation as validation sets) were used with 100 replications. The average predictive ability across statistical models and validation methods was about 0.49 for stem sweep, and 0.47 and 0.43 for total height and tree diameter, respectively. The sensitivity analysis suggested that prior densities (variance explained by markers) had little or no discernible effect on posterior means (residual variance) in Bayesian prediction models. Sampling from the progeny generation for model validation increased the predictive ability of markers for tree diameter and stem sweep but not for total height. The results are promising despite low linkage disequilibrium and low marker coverage of the genome (∼1.39 markers/cM).
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Affiliation(s)
- Fikret Isik
- INRA, UMR1202, BIOGECO, Cestas F-33610, France
| | - Jérôme Bartholomé
- INRA, UMR1202, BIOGECO, Cestas F-33610, France; Univ. Bordeaux, UMR1202, BIOGECO, Talence F-33170, France
| | - Alfredo Farjat
- Department of Statistics, North Carolina State University, Raleigh, NC, USA
| | - Emilie Chancerel
- INRA, UMR1202, BIOGECO, Cestas F-33610, France; Univ. Bordeaux, UMR1202, BIOGECO, Talence F-33170, France
| | - Annie Raffin
- INRA, UMR1202, BIOGECO, Cestas F-33610, France; Univ. Bordeaux, UMR1202, BIOGECO, Talence F-33170, France
| | | | - Christophe Plomion
- INRA, UMR1202, BIOGECO, Cestas F-33610, France; Univ. Bordeaux, UMR1202, BIOGECO, Talence F-33170, France
| | - Laurent Bouffier
- INRA, UMR1202, BIOGECO, Cestas F-33610, France; Univ. Bordeaux, UMR1202, BIOGECO, Talence F-33170, France.
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236
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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237
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Wang X, Wang L. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing. FRONTIERS IN PLANT SCIENCE 2016; 7:1350. [PMID: 27679641 PMCID: PMC5020087 DOI: 10.3389/fpls.2016.01350] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/23/2016] [Indexed: 05/19/2023]
Abstract
Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.
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Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species in China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- *Correspondence: Xuewen Wang
| | - Le Wang
- Key Laboratory of Forensic Genetics and Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public SecurityBeijing, China
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Syring JV, Tennessen JA, Jennings TN, Wegrzyn J, Scelfo-Dalbey C, Cronn R. Targeted Capture Sequencing in Whitebark Pine Reveals Range-Wide Demographic and Adaptive Patterns Despite Challenges of a Large, Repetitive Genome. FRONTIERS IN PLANT SCIENCE 2016; 7:484. [PMID: 27148310 PMCID: PMC4838605 DOI: 10.3389/fpls.2016.00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/25/2016] [Indexed: 05/20/2023]
Abstract
Whitebark pine (Pinus albicaulis) inhabits an expansive range in western North America, and it is a keystone species of subalpine environments. Whitebark is susceptible to multiple threats - climate change, white pine blister rust, mountain pine beetle, and fire exclusion - and it is suffering significant mortality range-wide, prompting the tree to be listed as 'globally endangered' by the International Union for Conservation of Nature and 'endangered' by the Canadian government. Conservation collections (in situ and ex situ) are being initiated to preserve the genetic legacy of the species. Reliable, transferrable, and highly variable genetic markers are essential for quantifying the genetic profiles of seed collections relative to natural stands, and ensuring the completeness of conservation collections. We evaluated the use of hybridization-based target capture to enrich specific genomic regions from the 27 GB genome of whitebark pine, and to evaluate genetic variation across loci, trees, and geography. Probes were designed to capture 7,849 distinct genes, and screening was performed on 48 trees. Despite the inclusion of repetitive elements in the probe pool, the resulting dataset provided information on 4,452 genes and 32% of targeted positions (528,873 bp), and we were able to identify 12,390 segregating sites from 47 trees. Variations reveal strong geographic trends in heterozygosity and allelic richness, with trees from the southern Cascade and Sierra Range showing the greatest distinctiveness and differentiation. Our results show that even under non-optimal conditions (low enrichment efficiency; inclusion of repetitive elements in baits), targeted enrichment produces high quality, codominant genotypes from large genomes. The resulting data can be readily integrated into management and gene conservation activities for whitebark pine, and have the potential to be applied to other members of 5-needle pine group (Pinus subsect. Quinquefolia) due to their limited genetic divergence.
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Affiliation(s)
- John V. Syring
- Department of Biology, Linfield College, McMinnvilleOR, USA
- *Correspondence: John V. Syring,
| | - Jacob A. Tennessen
- Department of Integrative Biology, Oregon State University, CorvallisOR, USA
| | - Tara N. Jennings
- Department of Botany and Plant Pathology, Oregon State University, CorvallisOR, USA
| | - Jill Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, StorrsCT, USA
| | - Camille Scelfo-Dalbey
- Jack Baskin School of Engineering, University of California, Santa Cruz, Santa CruzCA, USA
| | - Richard Cronn
- Pacific Northwest Research Station, United States Department of Agriculture, Forest Service, CorvallisOR, USA
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240
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Prunier J, Verta JP, MacKay JJ. Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. THE NEW PHYTOLOGIST 2016; 209:44-62. [PMID: 26206592 DOI: 10.1111/nph.13565] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/14/2015] [Indexed: 05/21/2023]
Abstract
Conifers have been understudied at the genomic level despite their worldwide ecological and economic importance but the situation is rapidly changing with the development of next generation sequencing (NGS) technologies. With NGS, genomics research has simultaneously gained in speed, magnitude and scope. In just a few years, genomes of 20-24 gigabases have been sequenced for several conifers, with several others expected in the near future. Biological insights have resulted from recent sequencing initiatives as well as genetic mapping, gene expression profiling and gene discovery research over nearly two decades. We review the knowledge arising from conifer genomics research emphasizing genome evolution and the genomic basis of adaptation, and outline emerging questions and knowledge gaps. We discuss future directions in three areas with potential inputs from NGS technologies: the evolutionary impacts of adaptation in conifers based on the adaptation-by-speciation model; the contributions of genetic variability of gene expression in adaptation; and the development of a broader understanding of genetic diversity and its impacts on genome function. These research directions promise to sustain research aimed at addressing the emerging challenges of adaptation that face conifer trees.
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Affiliation(s)
- Julien Prunier
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Jukka-Pekka Verta
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, Tübingen, 72076, Germany
| | - John J MacKay
- Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Quebec, QC, G1V 0A6, Canada
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241
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Trontin JF, Klimaszewska K, Morel A, Hargreaves C, Lelu-Walter MA. Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights. Methods Mol Biol 2016; 1359:167-207. [PMID: 26619863 DOI: 10.1007/978-1-4939-3061-6_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics.
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Affiliation(s)
- Jean-François Trontin
- FCBA, Pôle Biotechnologie et Sylviculture Avancée, Campus Forêt-Bois de Pierroton, 71 Route d'Arcachon, Cestas, 33610, France.
| | - Krystyna Klimaszewska
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., 10380, Stn. Sainte-Foy, QC, Canada, G1V 4C7
| | - Alexandre Morel
- INRA, UR 0588 Unité Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, CS 4001, Ardon, Orléans Cedex 2, 45075, France
| | | | - Marie-Anne Lelu-Walter
- INRA, UR 0588 Unité Amélioration, Génétique et Physiologie Forestières, 2163 Avenue de la Pomme de Pin, CS 4001, Ardon, Orléans Cedex 2, 45075, France
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242
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Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 2015; 125:683-99. [PMID: 26637996 PMCID: PMC5023732 DOI: 10.1007/s00412-015-0556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Sònia Garcia
- Laboratori de Botànica-Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Alena Kovarikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
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243
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Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin YC, Sjödin A, Van de Peer Y, Jansson S, Hvidsten TR, Street NR. The Plant Genome Integrative Explorer Resource: PlantGenIE.org. THE NEW PHYTOLOGIST 2015; 208:1149-56. [PMID: 26192091 DOI: 10.1111/nph.13557] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/08/2015] [Indexed: 05/18/2023]
Abstract
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
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Affiliation(s)
- David Sundell
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Sergiu Netotea
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Andreas Sjödin
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
- Department of Chemistry, Umeå University, SE-907 81, Umeå, Sweden
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, 0028, Pretoria, South Africa
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Torgeir R Hvidsten
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
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Muggli MD, Puglisi SJ, Ronen R, Boucher C. Misassembly detection using paired-end sequence reads and optical mapping data. Bioinformatics 2015; 31:i80-8. [PMID: 26072512 PMCID: PMC4542784 DOI: 10.1093/bioinformatics/btv262] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Motivation: A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method called misSEQuel that enhances the quality of draft genomes by identifying misassembly errors and their breakpoints using paired-end sequence reads and optical mapping data. Our method also fulfills the critical need for open source computational methods for analyzing optical mapping data. We apply our method to various assemblies of the loblolly pine, Francisella tularensis, rice and budgerigar genomes. We generated and used stimulated optical mapping data for loblolly pine and F.tularensis and used real optical mapping data for rice and budgerigar. Results: Our results demonstrate that we detect more than 54% of extensively misassembled contigs and more than 60% of locally misassembled contigs in assemblies of F.tularensis and between 31% and 100% of extensively misassembled contigs and between 57% and 73% of locally misassembled contigs in assemblies of loblolly pine. Using the real optical mapping data, we correctly identified 75% of extensively misassembled contigs and 100% of locally misassembled contigs in rice, and 77% of extensively misassembled contigs and 80% of locally misassembled contigs in budgerigar. Availability and implementation:misSEQuel can be used as a post-processing step in combination with any genome assembler and is freely available at http://www.cs.colostate.edu/seq/. Contact:muggli@cs.colostate.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin D Muggli
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Simon J Puglisi
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Roy Ronen
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christina Boucher
- Department of Computer Science, Colorado State University, Fort Collins, CO 80526, USA, Department of Computer Science, University of Helsinki, Finland and Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
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245
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Uddenberg D, Akhter S, Ramachandran P, Sundström JF, Carlsbecker A. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology. FRONTIERS IN PLANT SCIENCE 2015; 6:970. [PMID: 26579190 PMCID: PMC4630563 DOI: 10.3389/fpls.2015.00970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 05/20/2023]
Abstract
Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.
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Affiliation(s)
- Daniel Uddenberg
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Shirin Akhter
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
| | - Jens F. Sundström
- Department of Plant Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology, Uppsala BioCenter, Uppsala University, Uppsala, Sweden
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246
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Elliott TA, Gregory TR. What's in a genome? The C-value enigma and the evolution of eukaryotic genome content. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140331. [PMID: 26323762 PMCID: PMC4571570 DOI: 10.1098/rstb.2014.0331] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2015] [Indexed: 01/13/2023] Open
Abstract
Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60,000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of 'complete' genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.
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Affiliation(s)
- Tyler A Elliott
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - T Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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247
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de Miguel M, Bartholomé J, Ehrenmann F, Murat F, Moriguchi Y, Uchiyama K, Ueno S, Tsumura Y, Lagraulet H, de Maria N, Cabezas JA, Cervera MT, Gion JM, Salse J, Plomion C. Evidence of intense chromosomal shuffling during conifer evolution. Genome Biol Evol 2015; 7:2799-2809. [PMID: 26400405 PMCID: PMC4684699 DOI: 10.1093/gbe/evv185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although recent advances have been gained on genome evolution in angiosperm lineages, virtually nothing is known about karyotype evolution in the other group of seed plants, the gymnosperms. Here, we used high-density gene-based linkage mapping to compare the karyotype structure of two families of conifers (the most abundant group of gymnosperms) separated around 290 Ma: Pinaceae and Cupressaceae. We propose for the first time a model based on the fusion of 20 ancestral chromosomal blocks that may have shaped the modern karyotpes of Pinaceae (with n = 12) and Cupressaceae (with n = 11). The considerable difference in modern genome organization between these two lineages contrasts strongly with the remarkable level of synteny already reported within the Pinaceae. It also suggests a convergent evolutionary mechanism of chromosomal block shuffling that has shaped the genomes of the spermatophytes.
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Affiliation(s)
- Marina de Miguel
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Jérôme Bartholomé
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - François Ehrenmann
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Yoshinari Moriguchi
- Niigata University, Graduate School of Science and Technology, 8050, Igarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
| | - Kentaro Uchiyama
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- University of Tsukuba, Faculty of Life & Environmental Sciences, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hélène Lagraulet
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
| | - Nuria de Maria
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - José-Antonio Cabezas
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Maria-Teresa Cervera
- INIA-CIFOR, departamento de Ecologia y Genetica Forestal, 28040, Madrid, Spain INIA-UPM, Unidad mixta de Genomica y Ecofisiologia Forestal, Madrid, Spain
| | - Jean Marc Gion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France CIRAD, UMR AGAP, F-33612 Cestas, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC 'Génétique, Diversité et Ecophysiologie des Céréales', 5 Chemin de Beaulieu, 63100 Clermont Ferrand, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, 69 Route d'Arcachon,F-33610 Cestas, France Université de Bordeaux, UMR 1202 BIOGECO, F-33170 Talence, France
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248
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Zerbe P, Bohlmann J. Enzymes for synthetic biology of ambroxide-related diterpenoid fragrance compounds. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:427-47. [PMID: 25846965 DOI: 10.1007/10_2015_308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Ambrox and related ambroxides are highly priced in the fragrance industry, and valued for their delicate odor and fixative properties. Historically, ambrox was obtained from ambergris, a waxy excretion produced by sperm whales, now an endangered species. Synthetic ambroxides have replaced ambergris in perfume manufacture. Plant labdane diterpenoids can serve as starting material for ambroxide synthesis. Among these, the diterpene alcohol sclareol is the major industrial precursor obtained from cultivated clary sage (Salvia sclarea). In plants, a large family of diterpene synthase (diTPS) enzymes controls key reactions in diterpenoid biosynthesis. Advanced metabolite profiling and high-throughput sequencing of fragrant and medicinal plants have accelerated discovery of novel diTPS functions, providing a resource for combinatorial synthetic biology and metabolic engineering approaches. This chapter highlights recent progress on the discovery, characterization, and engineering of plant diTPSs with potential uses in ambroxide production. It features biosynthesis of sclareol, cis-abienol, and diterpene resin acids, as sources of genes and enzymes for diterpenoid bioproducts.
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Affiliation(s)
- Philipp Zerbe
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada,
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249
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Loziuk PL, Parker J, Li W, Lin CY, Wang JP, Li Q, Sederoff RR, Chiang VL, Muddiman DC. Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa. J Proteome Res 2015; 14:4158-68. [PMID: 26325666 DOI: 10.1021/acs.jproteome.5b00233] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.
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Affiliation(s)
- Philip L Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jennifer Parker
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Wei Li
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Vincent L Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - David C Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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250
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Cabezas JA, González-Martínez SC, Collada C, Guevara MA, Boury C, de María N, Eveno E, Aranda I, Garnier-Géré PH, Brach J, Alía R, Plomion C, Cervera MT. Nucleotide polymorphisms in a pine ortholog of the Arabidopsis degrading enzyme cellulase KORRIGAN are associated with early growth performance in Pinus pinaster. TREE PHYSIOLOGY 2015; 35:1000-1006. [PMID: 26093373 DOI: 10.1093/treephys/tpv050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
We have carried out a candidate-gene-based association genetic study in Pinus pinaster Aiton and evaluated the predictive performance for genetic merit gain of the most significantly associated genes and single nucleotide polymorphisms (SNPs). We used a second generation 384-SNP array enriched with candidate genes for growth and wood properties to genotype mother trees collected in 20 natural populations covering most of the European distribution of the species. Phenotypic data for total height, polycyclism, root-collar diameter and biomass were obtained from a replicated provenance-progeny trial located in two sites with contrasting environments (Atlantic vs Mediterranean climate). General linear models identified strong associations between growth traits (total height and polycyclism) and four SNPs from the korrigan candidate gene, after multiple testing corrections using false discovery rate. The combined genomic breeding value predictions assessed for the four associated korrigan SNPs by ridge regression-best linear unbiased prediction (RR-BLUP) and cross-validation accounted for up to 8 and 15% of the phenotypic variance for height and polycyclic growth, respectively, and did not improve adding SNPs from other growth-related candidate genes. For root-collar diameter and total biomass, they accounted for 1.6 and 1.1% of the phenotypic variance, respectively, but increased to 15 and 4.1% when other SNPs from lp3.1, lp3.3 and cad were included in RR-BLUP models. These results point towards a desirable integration of candidate-gene studies as a means to pre-select relevant markers, and aid genomic selection in maritime pine breeding programs.
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Affiliation(s)
- José Antonio Cabezas
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Santiago C González-Martínez
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Carmen Collada
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain Departamento de Biotecnología, ETSIM, Ciudad Universitaria s/n 28040 Madrid, Spain
| | - María Angeles Guevara
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Nuria de María
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Emmanuelle Eveno
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ismael Aranda
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Pauline H Garnier-Géré
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Jean Brach
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - Ricardo Alía
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France University of Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France
| | - María Teresa Cervera
- Department of Forest Ecology and Genetics, INIA-CIFOR, 28040 Madrid, Spain Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, 28040 Madrid, Spain
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