1
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Singh P, St Clair JB, Lind BM, Cronn R, Wilhelmi NP, Feau N, Lu M, Vidakovic DO, Hamelin RC, Shaw DC, Aitken SN, Yeaman S. Genetic architecture of disease resistance and tolerance in Douglas-fir trees. THE NEW PHYTOLOGIST 2024; 243:705-719. [PMID: 38803110 DOI: 10.1111/nph.19797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/18/2024] [Indexed: 05/29/2024]
Abstract
Understanding the genetic basis of how plants defend against pathogens is important to monitor and maintain resilient tree populations. Swiss needle cast (SNC) and Rhabdocline needle cast (RNC) epidemics are responsible for major damage of forest ecosystems in North America. Here we investigate the genetic architecture of tolerance and resistance to needle cast diseases in Douglas-fir (Pseudotsuga menziesii) caused by two fungal pathogens: SNC caused by Nothophaeocryptopus gaeumannii, and RNC caused by Rhabdocline pseudotsugae. We performed case-control genome-wide association analyses and found disease resistance and tolerance in Douglas-fir to be polygenic and under strong selection. We show that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection, and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identify a major transcriptional regulator of plant defense, ERF1, as the top candidate for RNC resistance. Our findings shed light on the highly polygenic architectures underlying fungal disease resistance and tolerance and have important implications for forestry and conservation as the climate changes.
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Affiliation(s)
- Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Aquatic Ecology & Evolution Division, Institute of Ecology and Evolution, University of Bern, Bern, CH-3012, Switzerland
- Department of Fish Ecology & Evolution, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, CH-6047, Switzerland
| | - J Bradley St Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Brandon M Lind
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Richard Cronn
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Nicholas P Wilhelmi
- Forest Health Protection, USDA Forest Service, Arizona Zone, Flagstaff, AZ, 86001, USA
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - David C Shaw
- Department of Forest Engineering, Resources and Management, Oregon State University, Corvallis, OR, 97331, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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2
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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Figueroa Corona L, Allen BJ, Puiu D, Wright J, De La Torre AR, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A genome sequence for the threatened whitebark pine. G3 (BETHESDA, MD.) 2024; 14:jkae061. [PMID: 38526344 PMCID: PMC11075562 DOI: 10.1093/g3journal/jkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Whitebark Pine Ecosystem Foundation, Missoula, MT 59808, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Meltzer
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- University of California Cooperative Extension, Central Sierra, Jackson, CA 95642, USA
| | - Daniela Puiu
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jessica Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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3
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Lind BM, Candido-Ribeiro R, Singh P, Lu M, Obreht Vidakovic D, Booker TR, Whitlock MC, Yeaman S, Isabel N, Aitken SN. How useful are genomic data for predicting maladaptation to future climate? GLOBAL CHANGE BIOLOGY 2024; 30:e17227. [PMID: 38558300 DOI: 10.1111/gcb.17227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 04/04/2024]
Abstract
Methods using genomic information to forecast potential population maladaptation to climate change or new environments are becoming increasingly common, yet the lack of model validation poses serious hurdles toward their incorporation into management and policy. Here, we compare the validation of maladaptation estimates derived from two methods-Gradient Forests (GFoffset) and the risk of non-adaptedness (RONA)-using exome capture pool-seq data from 35 to 39 populations across three conifer taxa: two Douglas-fir varieties and jack pine. We evaluate sensitivity of these algorithms to the source of input loci (markers selected from genotype-environment associations [GEA] or those selected at random). We validate these methods against 2- and 52-year growth and mortality measured in independent transplant experiments. Overall, we find that both methods often better predict transplant performance than climatic or geographic distances. We also find that GFoffset and RONA models are surprisingly not improved using GEA candidates. Even with promising validation results, variation in model projections to future climates makes it difficult to identify the most maladapted populations using either method. Our work advances understanding of the sensitivity and applicability of these approaches, and we discuss recommendations for their future use.
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Affiliation(s)
- Brandon M Lind
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rafael Candido-Ribeiro
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Dragana Obreht Vidakovic
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tom R Booker
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Quebec, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, Quebec, Canada
| | - Sally N Aitken
- Centre for Forest Conservation Genetics and Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Vu GTH, Cao HX, Hofmann M, Steiner W, Gailing O. Uncovering epigenetic and transcriptional regulation of growth in Douglas-fir: identification of differential methylation regions in mega-sized introns. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:863-875. [PMID: 37984804 PMCID: PMC10955500 DOI: 10.1111/pbi.14229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Tree growth performance can be partly explained by genetics, while a large proportion of growth variation is thought to be controlled by environmental factors. However, to what extent DNA methylation, a stable epigenetic modification, contributes to phenotypic plasticity in the growth performance of long-lived trees remains unclear. In this study, a comparative analysis of targeted DNA genotyping, DNA methylation and mRNAseq profiling for needles of 44-year-old Douglas-fir trees (Pseudotsuga menziesii (Mirb.) Franco) having contrasting growth characteristics was performed. In total, we identified 195 differentially expressed genes (DEGs) and 115 differentially methylated loci (DML) that are associated with genes involved in fitness-related processes such as growth, stress management, plant development and energy resources. Interestingly, all four intronic DML were identified in mega-sized (between 100 and 180 kbp in length) and highly expressed genes, suggesting specialized regulation mechanisms of these long intron genes in gymnosperms. DNA repetitive sequences mainly comprising long-terminal repeats of retroelements are involved in growth-associated DNA methylation regulation (both hyper- and hypomethylation) of 99 DML (86.1% of total DML). Furthermore, nearly 14% of the DML was not tagged by single nucleotide polymorphisms, suggesting a unique contribution of the epigenetic variation in tree growth.
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Affiliation(s)
- Giang Thi Ha Vu
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
| | - Martin Hofmann
- Nordwestdeutsche Forstliche VersuchsanstaltAbteilung WaldgenressourcenHann. MündenGermany
| | - Wilfried Steiner
- Nordwestdeutsche Forstliche VersuchsanstaltAbteilung WaldgenressourcenHann. MündenGermany
| | - Oliver Gailing
- Forest Genetics and Forest Tree BreedingUniversity of GöttingenGöttingenGermany
- Center for Integrated Breeding Research (CiBreed)University of GöttingenGöttingenGermany
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5
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Cui J, Li X, Lu Z, Jin B. Plant secondary metabolites involved in the stress tolerance of long-lived trees. TREE PHYSIOLOGY 2024; 44:tpae002. [PMID: 38196002 DOI: 10.1093/treephys/tpae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/29/2023] [Indexed: 01/11/2024]
Abstract
Ancient trees are natural wonders because of their longevity, having lived for hundreds or thousands of years, and their ability to withstand changing environments and a variety of stresses. These long-lived trees have sophisticated defense mechanisms, such as the production of specialized plant metabolites (SPMs). In this review, we provide an overview of the major biotic and abiotic stresses that long-lived trees often face, as well as an analysis of renowned ancient tree species and their unique protective SPMs against environmental stressors. We also discuss the synthesis and accumulation of defensive SPMs induced by environmental factors and endophytes in these trees. Furthermore, we conducted a comparative genomic analysis of 17 long-lived tree species and discovered significant expansions of SPM biosynthesis gene families in these species. Our comprehensive review reveals the crucial role of SPMs in high resistance in long-lived trees, providing a novel natural resource for plant defense, crop improvement and even the pharmaceutical industry.
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Affiliation(s)
- Jiawen Cui
- College of Horticulture and Landscape, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China
| | - Xiang Li
- College of Horticulture and Landscape, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China
| | - Zhaogeng Lu
- College of Horticulture and Landscape, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China
| | - Biao Jin
- College of Horticulture and Landscape, Yangzhou University, 48 East Wenhui Road, Yangzhou 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College, Yangzhou University, 48 East Wenhui Road, Yangzhou, China
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6
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Ousmael K, Whetten RW, Xu J, Nielsen UB, Lamour K, Hansen OK. Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach). Sci Rep 2023; 13:22488. [PMID: 38110478 PMCID: PMC10728141 DOI: 10.1038/s41598-023-49462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.
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Affiliation(s)
- Kedra Ousmael
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27606, USA
| | - Jing Xu
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ulrik B Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ole K Hansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
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7
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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Corona LF, Allen BJ, Puiu D, Wright J, Torre ARDL, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A Genome Sequence for the Threatened Whitebark Pine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567420. [PMID: 38014212 PMCID: PMC10680812 DOI: 10.1101/2023.11.16.567420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Whitebark pine (WBP, Pinus albicaulis ) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola ) and additional threats from mountain pine beetle ( Dendroctonus ponderosae ), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short-reads of haploid megametophyte tissue and Oxford Nanopore long-reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gbp of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gbp). Approximately 87.2% (24.0 Gbp) of total sequence was placed on the twelve WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich-repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the three subclasses of NLRs (TNL, CNL, RNL). Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo assembled transcriptomes.
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8
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Teyssier C, Rogier O, Claverol S, Gautier F, Lelu-Walter MA, Duruflé H. Comprehensive Organ-Specific Profiling of Douglas Fir ( Pseudotsuga menziesii) Proteome. Biomolecules 2023; 13:1400. [PMID: 37759800 PMCID: PMC10526743 DOI: 10.3390/biom13091400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.
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Affiliation(s)
| | - Odile Rogier
- INRAE, ONF, BioForA, UMR 0588, 45075 Orleans, France
| | - Stéphane Claverol
- Plateforme de Protéomique, Université de Bordeaux, 33405 Bordeaux, France
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9
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Velasco VME, Ferreira A, Zaman S, Noordermeer D, Ensminger I, Wegrzyn JL. A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir). G3 (BETHESDA, MD.) 2023; 13:jkac304. [PMID: 36454025 PMCID: PMC10468028 DOI: 10.1093/g3journal/jkac304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/13/2021] [Accepted: 10/19/2022] [Indexed: 12/02/2022]
Abstract
Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber tree. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under nonstress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used 2 computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long noncoding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.
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Affiliation(s)
| | - Alyssa Ferreira
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Sumaira Zaman
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
| | - Devin Noordermeer
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto,
Mississauga, ON L5L 1C8, Canada
- Graduate Department of Cell and Systems Biology, University of
Toronto, Toronto, ON M5S, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of
Toronto, Toronto, ON M5S, Canada
| | - Jill L Wegrzyn
- Department of Evolution and Ecology, University of
Connecticut, Storrs, CT 06269, USA
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10
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Jing Y, Bian L, Zhang X, Zhao B, Zheng R, Su S, Ye D, Zheng X, El-Kassaby YA, Shi J. Genetic diversity and structure of the 4 th cycle breeding population of Chinese fir ( Cunninghamia lanceolata (lamb.) hook). FRONTIERS IN PLANT SCIENCE 2023; 14:1106615. [PMID: 36778690 PMCID: PMC9911867 DOI: 10.3389/fpls.2023.1106615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi ) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.
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Affiliation(s)
- Yonglian Jing
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Bian
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuefeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Benwen Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Shunde Su
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Daiquan Ye
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Xueyan Zheng
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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11
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Scutt CP. Model Species to Investigate the Origin of Flowers. Methods Mol Biol 2023; 2686:83-109. [PMID: 37540355 DOI: 10.1007/978-1-0716-3299-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.
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Affiliation(s)
- Charles P Scutt
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.
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12
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Mishima K, Hirakawa H, Iki T, Fukuda Y, Hirao T, Tamura A, Takahashi M. Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica). BMC PLANT BIOLOGY 2022; 22:470. [PMID: 36192701 PMCID: PMC9531402 DOI: 10.1186/s12870-022-03862-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Japanese larch (Larix kaempferi) is an economically important deciduous conifer species that grows in cool-temperate forests and is endemic to Japan. Kuril larch (L. gmelinii var. japonica) is a variety of Dahurian larch that is naturally distributed in the Kuril Islands and Sakhalin. The hybrid larch (L. gmelinii var. japonica × L. kaempferi) exhibits heterosis, which manifests as rapid juvenile growth and high resistance to vole grazing. Since these superior characteristics have been valued by forestry managers, the hybrid larch is one of the most important plantation species in Hokkaido. To accelerate molecular breeding in these species, we collected and compared full-length cDNA isoforms (Iso-Seq) and RNA-Seq short-read, and merged them to construct candidate gene as reference for both Larix species. To validate the results, candidate protein-coding genes (ORFs) related to some flowering signal-related genes were screened from the reference sequences, and the phylogenetic relationship with closely related species was elucidated. RESULTS Using the isoform sequencing of PacBio RS ll and the de novo assembly of RNA-Seq short-read sequences, we identified 50,690 and 38,684 ORFs in Japanese larch and Kuril larch, respectively. BUSCO completeness values were 90.5% and 92.1% in the Japanese and Kuril larches, respectively. After comparing the collected ORFs from the two larch species, a total of 19,813 clusters, comprising 22,571 Japanese larch ORFs and 22,667 Kuril larch ORFs, were contained in the intersection of the Venn diagram. In addition, we screened several ORFs related to flowering signals (SUPPRESSER OF OVEREXPRESSION OF CO1: SOC1, LEAFY: LFY, FLOWERING Locus T: FT, CONSTANCE: CO) from both reference sequences, and very similar found in other species. CONCLUSIONS The collected ORFs will be useful as reference sequences for molecular breeding of Japanese and Kuril larches, and also for clarifying the evolution of the conifer genome and investigating functional genomics.
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Affiliation(s)
- Kentaro Mishima
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 95 Osaki, Takizawa, Iwate, 020-0621, Japan.
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Taiichi Iki
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 95 Osaki, Takizawa, Iwate, 020-0621, Japan
| | - Yoko Fukuda
- Hokkaido Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 561-1 Bunkyodaimidorimachi, Ebetsu, Hokkaido, 069-0836, Japan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Akira Tamura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
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13
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
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14
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Wan T, Gong Y, Liu Z, Zhou Y, Dai C, Wang Q. Evolution of complex genome architecture in gymnosperms. Gigascience 2022; 11:6659718. [PMID: 35946987 PMCID: PMC9364684 DOI: 10.1093/gigascience/giac078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Gymnosperms represent an ancient lineage that diverged from early spermatophytes during the Devonian. The long fossil records and low diversity in living species prove their complex evolutionary history, which included ancient radiations and massive extinctions. Due to their ultra-large genome size, the whole-genome assembly of gymnosperms has only generated in the past 10 years and is now being further expanded into more taxonomic representations. Here, we provide an overview of the publicly available gymnosperm genome resources and discuss their assembly quality and recent findings in large genome architectures. In particular, we describe the genomic features most related to changes affecting the whole genome. We also highlight new realizations relative to repetitive sequence dynamics, paleopolyploidy, and long introns. Based on the results of relevant genomic studies of gymnosperms, we suggest additional efforts should be made toward exploring the genomes of medium-sized (5–15 gigabases) species. Lastly, more comparative analyses among high-quality assemblies are needed to understand the genomic shifts and the early species diversification of seed plants.
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Affiliation(s)
- Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China.,Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - Yanbing Gong
- Department of Ecology, Tibetan Centre for Ecology and Conservation at WHU-TU, State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Research Center for Ecology, College of Science, Tibet University, Lhasa 850000, China
| | - Zhiming Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen 518004, China
| | - YaDong Zhou
- School of Life Science, Nanchang University, Nanchang 330031, China
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | - Qingfeng Wang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan 430074, China
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15
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Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae. PLANTS 2022; 11:plants11152062. [PMID: 35956540 PMCID: PMC9370799 DOI: 10.3390/plants11152062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies.
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16
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Conifer Biotechnology: An Overview. FORESTS 2022. [DOI: 10.3390/f13071061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The peculiar characteristics of conifers determine the difficulty of their study and their great importance from various points of view. However, their study faces numerous important scientific, methodological, cultural, economic, social, and legal challenges. This paper presents an approach to several of those challenges and proposes a multidisciplinary scientific perspective that leads to a holistic understanding of conifers from the perspective of the latest technical, computer, and scientific advances. This review highlights the deep connection that all scientific contributions to conifers can have in each other as fully interrelated communicating vessels.
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17
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Sun C, Xie YH, Li Z, Liu YJ, Sun XM, Li JJ, Quan WP, Zeng QY, Van de Peer Y, Zhang SG. The Larix kaempferi genome reveals new insights into wood properties. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1364-1373. [PMID: 35442564 DOI: 10.1111/jipb.13265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jing-Jing Li
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Wei-Peng Quan
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa
| | - Shou-Gong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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18
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Bowles AMC, Paps J, Bechtold U. Water-related innovations in land plants evolved by different patterns of gene cooption and novelty. THE NEW PHYTOLOGIST 2022; 235:732-742. [PMID: 35048381 PMCID: PMC9303528 DOI: 10.1111/nph.17981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/25/2021] [Indexed: 05/26/2023]
Abstract
The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.
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Affiliation(s)
- Alexander M. C. Bowles
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Geographical SciencesUniversity of BristolUniversity RoadBristolBS8 1RLUK
| | - Jordi Paps
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- School of Biological SciencesUniversity of Bristol24 Tyndall AvenueBristolBS8 1TQUK
| | - Ulrike Bechtold
- School of Life SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Present address:
Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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19
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Valderrama‐Martín JM, Ortigosa F, Ávila C, Cánovas FM, Hirel B, Cantón FR, Cañas RA. A revised view on the evolution of glutamine synthetase isoenzymes in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:946-960. [PMID: 35199893 PMCID: PMC9310647 DOI: 10.1111/tpj.15712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/09/2022] [Accepted: 02/17/2022] [Indexed: 05/29/2023]
Abstract
Glutamine synthetase (GS) is a key enzyme responsible for the incorporation of inorganic nitrogen in the form of ammonium into the amino acid glutamine. In plants, two groups of functional GS enzymes are found: eubacterial GSIIb (GLN2) and eukaryotic GSIIe (GLN1/GS). Only GLN1/GS genes are found in vascular plants, which suggests that they are involved in the final adaptation of plants to terrestrial life. The present phylogenetic study reclassifies the different GS genes of seed plants into three clusters: GS1a, GS1b and GS2. The presence of genes encoding GS2 has been expanded to Cycadopsida gymnosperms, which suggests the origin of this gene in a common ancestor of Cycadopsida, Ginkgoopsida and angiosperms. GS1a genes have been identified in all gymnosperms, basal angiosperms and some Magnoliidae species. Previous studies in conifers and the gene expression profiles obtained in ginkgo and magnolia in the present work could explain the absence of GS1a in more recent angiosperm species (e.g. monocots and eudicots) as a result of the redundant roles of GS1a and GS2 in photosynthetic cells. Altogether, the results provide a better understanding of the evolution of plant GS isoenzymes and their physiological roles, which is valuable for improving crop nitrogen use efficiency and productivity. This new view of GS evolution in plants, including a new cytosolic GS group (GS1a), has important functional implications in the context of plant metabolism adaptation to global changes.
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Affiliation(s)
- José Miguel Valderrama‐Martín
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y BioquímicaUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
- Integrative Molecular Biology LabUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
| | - Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y BioquímicaUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y BioquímicaUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
| | - Francisco M. Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y BioquímicaUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
| | - Bertrand Hirel
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Centre de Versailles‐GrignonRD 1078026Versailles CedexFrance
| | - Francisco R. Cantón
- Integrative Molecular Biology LabUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
| | - Rafael A. Cañas
- Integrative Molecular Biology LabUniversidad de Málaga, Campus Universitario de Teatinos29071MálagaSpain
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20
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Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers. FORESTS 2022. [DOI: 10.3390/f13040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The global change scenarios highlight the urgency of clarifying the mechanisms driving the determination of wood traits in forest trees. Coniferous xylem is characterized by the alternation between earlywood (EW) and latewood (LW), on which proportions the wood density depend, one of the most important mechanical xylem qualities. However, the molecular mechanisms triggering the transition between the production of cells with the typical features of EW to the LW are still far from being completely elucidated. The increasing availability of omics resources for conifers, e.g., genomes and transcriptomes, would lay the basis for the comprehension of wood formation dynamics, boosting both breeding and gene-editing approaches. This review is intended to introduce the importance of wood formation dynamics and xylem traits of conifers in a changing environment. Then, an up-to-date overview of the omics resources available for conifers was reported, focusing on both genomes and transcriptomes. Later, an analysis of wood formation studies using omics approaches was conducted, with the aim of elucidating the main metabolic pathways involved in EW and LW determination. Finally, the future perspectives and the urgent needs on this research topic were highlighted.
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21
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Cao HX, Vu GTH, Gailing O. From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees. Int J Mol Sci 2022; 23:966. [PMID: 35055150 PMCID: PMC8780650 DOI: 10.3390/ijms23020966] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/11/2022] Open
Abstract
Due to the economic and ecological importance of forest trees, modern breeding and genetic manipulation of forest trees have become increasingly prevalent. The CRISPR-based technology provides a versatile, powerful, and widely accepted tool for analyzing gene function and precise genetic modification in virtually any species but remains largely unexplored in forest species. Rapidly accumulating genetic and genomic resources for forest trees enabled the identification of numerous genes and biological processes that are associated with important traits such as wood quality, drought, or pest resistance, facilitating the selection of suitable gene editing targets. Here, we introduce and discuss the latest progress, opportunities, and challenges of genome sequencing and editing for improving forest sustainability.
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Affiliation(s)
- Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Giang Thi Ha Vu
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Gottingen, Germany;
- Center for Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Gottingen, Germany
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22
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Neale DB, Zimin AV, Zaman S, Scott AD, Shrestha B, Workman RE, Puiu D, Allen BJ, Moore ZJ, Sekhwal MK, De La Torre AR, McGuire PE, Burns E, Timp W, Wegrzyn JL, Salzberg SL. Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 (BETHESDA, MD.) 2022; 12:6460957. [PMID: 35100403 PMCID: PMC8728005 DOI: 10.1093/g3journal/jkab380] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Department of Computer Science & Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Alison D Scott
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Rachael E Workman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Zane J Moore
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Manoj K Sekhwal
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Emily Burns
- Save the Redwoods League, San Francisco, CA 94104, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
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23
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Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change. Int J Mol Sci 2021; 22:ijms222413524. [PMID: 34948318 PMCID: PMC8703565 DOI: 10.3390/ijms222413524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.
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24
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Pervaiz T, Liu SW, Uddin S, Amjid MW, Niu SH, Wu HX. The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis. Int J Mol Sci 2021; 22:ijms22179604. [PMID: 34502511 PMCID: PMC8431770 DOI: 10.3390/ijms22179604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/11/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.
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Affiliation(s)
- Tariq Pervaiz
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Shuang-Wei Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Saleem Uddin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
| | - Muhammad Waqas Amjid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China;
| | - Shi-Hui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
- Correspondence: (S.-H.N.); (H.X.W.)
| | - Harry X. Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (T.P.); (S.-W.L.); (S.U.)
- Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus vag 6, SE-901 83 Umea, Sweden
- CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT 2601, Australia
- Correspondence: (S.-H.N.); (H.X.W.)
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25
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Lind BM, Lu M, Obreht Vidakovic D, Singh P, Booker TR, Aitken SN, Yeaman S. Haploid, diploid, and pooled exome capture recapitulate features of biology and paralogy in two non-model tree species. Mol Ecol Resour 2021; 22:225-238. [PMID: 34270863 PMCID: PMC9292622 DOI: 10.1111/1755-0998.13474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/18/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022]
Abstract
Despite their suitability for studying evolution, many conifer species have large and repetitive giga‐genomes (16–31 Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost‐saving benefits of pool‐seq and exome‐capture to discover SNPs in two conifer species, Douglas‐fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (r > .948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > .973). Our work addresses bioinformatic challenges in non‐model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool‐seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.
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Affiliation(s)
- Brandon M Lind
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Tom R Booker
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada.,Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, Centre for Forest Conservation Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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26
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Heitkam T, Schulte L, Weber B, Liedtke S, Breitenbach S, Kögler A, Morgenstern K, Brückner M, Tröber U, Wolf H, Krabel D, Schmidt T. Comparative Repeat Profiling of Two Closely Related Conifers ( Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. Front Genet 2021; 12:683668. [PMID: 34322154 PMCID: PMC8312256 DOI: 10.3389/fgene.2021.683668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Luise Schulte
- Institute of Botany, Technische Universität Dresden, Dresden, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Sarah Breitenbach
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kristin Morgenstern
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | | | - Ute Tröber
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Heino Wolf
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Doris Krabel
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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27
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Olsson S, Lorenzo Z, Zabal-Aguirre M, Piotti A, Vendramin GG, González-Martínez SC, Grivet D. Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches. PLANT MOLECULAR BIOLOGY 2021; 106:367-380. [PMID: 33934278 DOI: 10.1007/s11103-021-01155-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Complementary gene-resequencing and transcriptomic approaches reveal contrasted evolutionary histories in a species complex. Pinus halepensis and Pinus brutia are closely related species that can intercross, but occupy different geographical ranges and bioclimates. To study the evolution of this species complex and to provide genomic resources for further research, we produce and analyze two new complementary sets of genetic resources: (i) a set of 172 re-sequenced genomic target loci analyzed in 45 individuals, and (ii) a set of 11 transcriptome assemblies. These two datasets provide insights congruent with previous studies: P. brutia displays high level of genetic diversity and no genetic sub-structure, while P. halepensis shows three main genetic clusters, the western Mediterranean and North African clusters displaying much lower genetic diversity than the eastern Mediterranean cluster, the latter cluster having similar genetic diversity to P. brutia. In addition, these datasets provide new insights on the timing of the species-complex history: the two species would have split at the end of the tertiary, and the changing climatic conditions of the Mediterranean region at the end of the Tertiary-beginning of the Quaternary, together with the distinct species tolerance to harsh climatic conditions would have resulted in different geographic distributions, demographic histories and genetic patterns of the two pines. The multiple glacial-interglacial cycles during the Quaternary would have led to the expansion of P. brutia in the Middle East, while P. halepensis would have been through bottlenecks. The last glaciations, from 0.6 Mya on, would have affected further the Western genetic pool of P. halepensis.
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Affiliation(s)
- Sanna Olsson
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
| | - Zaida Lorenzo
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Mario Zabal-Aguirre
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, Division of Florence, National Research Council, 50019, Sesto Fiorentino, Florence, Italy
| | - Santiago C González-Martínez
- UMR BIOGECO, INRAE, University of Bordeaux, 33610, Cestas, France
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain
| | - Delphine Grivet
- Department of Forest Ecology & Genetics, Forest Research Centre, INIA-CSIC, Carretera de la Coruña km 7.5, 28040, Madrid, Spain.
- Sustainable Forest Management Research Institute, INIA - University of Valladolid, Avda. Madrid 44, 34004, Palencia, Spain.
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28
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George J, Schueler S, Grabner M, Karanitsch‐Ackerl S, Mayer K, Stierschneider M, Weissenbacher L, van Loo M. Looking for the needle in a downsized haystack: Whole-exome sequencing unravels genomic signals of climatic adaptation in Douglas-fir ( Pseudotsuga menziesii). Ecol Evol 2021; 11:8238-8253. [PMID: 34188883 PMCID: PMC8216971 DOI: 10.1002/ece3.7654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/14/2021] [Accepted: 04/21/2021] [Indexed: 11/24/2022] Open
Abstract
Conifers often occur along steep gradients of diverse climates throughout their natural ranges, which is expected to result in spatially varying selection to local climate conditions. However, signals of climatic adaptation can often be confounded, because unraveled clines covary with signals caused by neutral evolutionary processes such as gene flow and genetic drift. Consequently, our understanding of how selection and gene flow have shaped phenotypic and genotypic differentiation in trees is still limited.A 40-year-old common garden experiment comprising 16 Douglas-fir (Pseudotsuga menziesii) provenances from a north-to-south gradient of approx. 1,000 km was analyzed, and genomic information was obtained from exome capture, which resulted in an initial genomic dataset of >90,000 single nucleotide polymorphisms. We used a restrictive and conservative filtering approach, which permitted us to include only SNPs and individuals in environmental association analysis (EAA) that were free of potentially confounding effects (LD, relatedness among trees, heterozygosity deficiency, and deviations from Hardy-Weinberg proportions). We used four conceptually different genome scan methods based on FST outlier detection and gene-environment association in order to disentangle truly adaptive SNPs from neutral SNPs.We found that a relatively small proportion of the exome showed a truly adaptive signal (0.01%-0.17%) when population substructuring and multiple testing was accounted for. Nevertheless, the unraveled SNP candidates showed significant relationships with climate at provenance origins, which strongly suggests that they have featured adaptation in Douglas-fir along a climatic gradient. Two SNPs were independently found by three of the employed algorithms, and one of them is in close proximity to an annotated gene involved in circadian clock control and photoperiodism as was similarly found in Populus balsamifera. Synthesis. We conclude that despite neutral evolutionary processes, phenotypic and genomic signals of adaptation to climate are responsible for differentiation, which in particular explain disparity between the well-known coastal and interior varieties of Douglas-fir.
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Affiliation(s)
- Jan‐Peter George
- Faculty of Science & TechnologyTartu ObservatoryUniversity of TartuTartuEstonia
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Silvio Schueler
- Department of Forest Growth, Silviculture and GeneticsAustrian Research Centre for ForestsViennaAustria
| | - Michael Grabner
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Sandra Karanitsch‐Ackerl
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | - Konrad Mayer
- Institute of Wood Science and TechnologyUniversity of Natural Resources and Life Sciences (BOKU)TullnAustria
| | | | - Lambert Weissenbacher
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and Genetics/Unit of provenance research and breedingAustrian Research Centre for ForestsViennaAustria
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29
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Ranade SS, Egertsdotter U. In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack LEC2, one of the key regulators of initiation of the process. BMC Genomics 2021; 22:392. [PMID: 34039265 PMCID: PMC8157724 DOI: 10.1186/s12864-021-07718-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/12/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. RESULTS Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM, LEC1, LEC1-LIKE, LEC2 and FUSCA3, based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea (Picea abies) and Pinus (Pinus taeda), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). CONCLUSIONS This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda, the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden.
| | - Ulrika Egertsdotter
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center (UPSC), Swedish University of Agricultural Science (SLU), 901 83, Umeå, Sweden
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30
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Matallana-Ramirez LP, Whetten RW, Sanchez GM, Payn KG. Breeding for Climate Change Resilience: A Case Study of Loblolly Pine ( Pinus taeda L.) in North America. FRONTIERS IN PLANT SCIENCE 2021; 12:606908. [PMID: 33995428 PMCID: PMC8119900 DOI: 10.3389/fpls.2021.606908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 04/08/2021] [Indexed: 05/25/2023]
Abstract
Earth's atmosphere is warming and the effects of climate change are becoming evident. A key observation is that both the average levels and the variability of temperature and precipitation are changing. Information and data from new technologies are developing in parallel to provide multidisciplinary opportunities to address and overcome the consequences of these changes in forest ecosystems. Changes in temperature and water availability impose multidimensional environmental constraints that trigger changes from the molecular to the forest stand level. These can represent a threat for the normal development of the tree from early seedling recruitment to adulthood both through direct mortality, and by increasing susceptibility to pathogens, insect attack, and fire damage. This review summarizes the strengths and shortcomings of previous work in the areas of genetic variation related to cold and drought stress in forest species with particular emphasis on loblolly pine (Pinus taeda L.), the most-planted tree species in North America. We describe and discuss the implementation of management and breeding strategies to increase resilience and adaptation, and discuss how new technologies in the areas of engineering and genomics are shaping the future of phenotype-genotype studies. Lessons learned from the study of species important in intensively-managed forest ecosystems may also prove to be of value in helping less-intensively managed forest ecosystems adapt to climate change, thereby increasing the sustainability and resilience of forestlands for the future.
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Affiliation(s)
- Lilian P. Matallana-Ramirez
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Georgina M. Sanchez
- Center for Geospatial Analytics, North Carolina State University, Raleigh, Raleigh, NC, United States
| | - Kitt G. Payn
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, Raleigh, NC, United States
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Wei FJ, Ueno S, Ujino-Ihara T, Saito M, Tsumura Y, Higuchi Y, Hirayama S, Iwai J, Hakamata T, Moriguchi Y. Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1). PLoS One 2021; 16:e0247180. [PMID: 33630910 PMCID: PMC7935350 DOI: 10.1371/journal.pone.0247180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 02/02/2021] [Indexed: 11/18/2022] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an important conifer used for afforestation in Japan. As the genome of this species is 11 Gbps, it is too large to assemble within a short timeframe. Transcriptomics is one approach that can address this deficiency. Here we designed a workflow consisting of three stages to de novo assemble transcriptome using Oases and Trinity. The three transcriptomic stage used were independent assembly, automatic and semi-manual integration, and refinement by filtering out potential contamination. We identified a set of 49,795 cDNA and an equal number of translated proteins. According to the benchmark set by BUSCO, 87.01% of cDNAs identified were complete genes, and 78.47% were complete and single-copy genes. Compared to other full-length cDNA resources collected by Sanger and PacBio sequencers, the extent of the coverage in our dataset was the highest, indicating that these data can be safely used for further studies. When two tissue-specific libraries were compared, there were significant expression differences between male strobili and leaf and bark sets. Moreover, subtle expression difference between male-fertile and sterile libraries were detected. Orthologous genes from other model plants and conifer species were identified. We demonstrated that our transcriptome assembly output (CJ3006NRE) can serve as a reference transcriptome for future functional genomics and evolutionary biology studies.
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Affiliation(s)
- Fu-Jin Wei
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
- * E-mail:
| | - Tokuko Ujino-Ihara
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
| | - Maki Saito
- Forest Research Institute, Toyama Prefectural Agricultural Forestry and Fisheries Research Center, Toyama, Japan
| | - Yoshihiko Tsumura
- Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Yuumi Higuchi
- Niigata Prefectural Forest Research Institute, Niigata, Japan
| | | | - Junji Iwai
- Niigata Prefectural Forest Research Institute, Niigata, Japan
| | - Tetsuji Hakamata
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Shizuoka, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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Di Stilio VS, Ickert-Bond SM. Ephedra as a gymnosperm evo-devo model lineage. Evol Dev 2021; 23:256-266. [PMID: 33503333 DOI: 10.1111/ede.12370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/29/2020] [Accepted: 01/02/2021] [Indexed: 11/28/2022]
Abstract
Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.
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Probabilistic Provenance Detection and Management Pathways for Pseudotsuga menziesii (Mirb.) Franco in Italy Using Climatic Analogues. PLANTS 2021; 10:plants10020215. [PMID: 33498675 PMCID: PMC7912538 DOI: 10.3390/plants10020215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022]
Abstract
The introduction of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] in Europe has been one of the most important and extensive silvicultural experiments since the 1850s. This success was mainly supported by the species’ wide genome and phenotypic plasticity even if the genetic origin of seeds used for plantations is nowadays often unknown. This is especially true for all the stands planted before the IUFRO experimentation in the 1960s. In this paper, a methodology to estimate the Douglas-fir provenances currently growing in Italy is proposed. The raw data from the last Italian National Forest Inventory were combined with literature information to obtain the current spatial distribution of the species in the country representing its successful introduction. Afterwards, a random forest classification model was run using downscaled climatic data as predictors and the classification scheme adopted in previous research studies in the Pacific North West of America. The analysis highlighted good matching between the native and the introduction range in Italy. Coastal provenances from British Columbia and the dry coast of Washington were detected as the most likely seed sources, covering 63.4% and 33.8% of the current distribution of the species in the country, respectively. Interior provenances and those from the dry coast of Oregon were also represented but limited to very few cases. The extension of the model on future scenarios predicted a gradual shift in suitable provenances with the dry coast of Oregon in the mid-term (2050s) and afterwards California (2080s) being highlighted as possible new seed sources. However, only further analysis with genetic markers and molecular methods will be able to confirm the proposed scenarios. A validation of the genotypes currently available in Italy will be mandatory as well as their regeneration processes (i.e., adaptation), which may also diverge from those occurring in the native range due to a different environmental pressure. This new information will also add important knowledge, allowing a refinement of the proposed modeling framework for a better support for forest managers.
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De La Torre AR, Wilhite B, Puiu D, St. Clair JB, Crepeau MW, Salzberg SL, Langley CH, Allen B, Neale DB. Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir. Genes (Basel) 2021; 12:110. [PMID: 33477542 PMCID: PMC7831106 DOI: 10.3390/genes12010110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023] Open
Abstract
Understanding the genomic and environmental basis of cold adaptation is key to understand how plants survive and adapt to different environmental conditions across their natural range. Univariate and multivariate genome-wide association (GWAS) and genotype-environment association (GEA) analyses were used to test associations among genome-wide SNPs obtained from whole-genome resequencing, measures of growth, phenology, emergence, cold hardiness, and range-wide environmental variation in coastal Douglas-fir (Pseudotsuga menziesii). Results suggest a complex genomic architecture of cold adaptation, in which traits are either highly polygenic or controlled by both large and small effect genes. Newly discovered associations for cold adaptation in Douglas-fir included 130 genes involved in many important biological functions such as primary and secondary metabolism, growth and reproductive development, transcription regulation, stress and signaling, and DNA processes. These genes were related to growth, phenology and cold hardiness and strongly depend on variation in environmental variables such degree days below 0c, precipitation, elevation and distance from the coast. This study is a step forward in our understanding of the complex interconnection between environment and genomics and their role in cold-associated trait variation in boreal tree species, providing a baseline for the species' predictions under climate change.
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Affiliation(s)
- Amanda R. De La Torre
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Benjamin Wilhite
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll, Flagstaff, AZ 86011, USA;
| | - Daniela Puiu
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - John Bradley St. Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331, USA;
| | - Marc W. Crepeau
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Steven L. Salzberg
- Center for Computational Biology, Department of Biomedical Engineering, Computer Science and Biostatistics, John Hopkins University, 3100 Wyman Park Dr, Wyman Park Building, Room S220, Baltimore, MD 21211, USA; (D.P.); (S.L.S.)
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (M.W.C.); (C.H.L.)
| | - Brian Allen
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
| | - David B. Neale
- Department of Plant Sciences, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA; (B.A.); (D.B.N.)
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García-García I, Méndez-Cea B, Martín-Gálvez D, Seco JI, Gallego FJ, Linares JC. Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline. FRONTIERS IN PLANT SCIENCE 2021; 12:797958. [PMID: 35058957 PMCID: PMC8764141 DOI: 10.3389/fpls.2021.797958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/13/2021] [Indexed: 05/14/2023]
Abstract
Forest tree species are highly vulnerable to the effects of climate change. As sessile organisms with long generation times, their adaptation to a local changing environment may rely on epigenetic modifications when allele frequencies are not able to shift fast enough. However, the current lack of knowledge on this field is remarkable, due to many challenges that researchers face when studying this issue. Huge genome sizes, absence of reference genomes and annotation, and having to analyze huge amounts of data are among these difficulties, which limit the current ability to understand how climate change drives tree species epigenetic modifications. In spite of this challenging framework, some insights on the relationships among climate change-induced stress and epigenomics are coming. Advances in DNA sequencing technologies and an increasing number of studies dealing with this topic must boost our knowledge on tree adaptive capacity to changing environmental conditions. Here, we discuss challenges and perspectives in the epigenetics of climate change-induced forests decline, aiming to provide a general overview of the state of the art.
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Affiliation(s)
- Isabel García-García
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Isabel García-García,
| | - Belén Méndez-Cea
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
- Belén Méndez-Cea,
| | - David Martín-Gálvez
- Departamento de Biodiversidad, Ecología y Evolución, UD Zoología, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - José Ignacio Seco
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Francisco Javier Gallego
- Departamento de Genética, Fisiología y Microbiología, UD Genética, Facultad de CC Biológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan Carlos Linares
- Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
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Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX. Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species. Mol Ecol Resour 2020; 21:880-896. [PMID: 33179386 PMCID: PMC7984398 DOI: 10.1111/1755-0998.13292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022]
Abstract
Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome‐wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS‐based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two‐step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high‐confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high‐quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
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Affiliation(s)
- Carolina Bernhardsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Yanjun Zan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden.,Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Black Mountain Laboratory, CSIRO National Research Collection Australia, Canberra, ACT, Australia
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Abstract
The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains. Genomic data are limited in giant sequoia and producing a reference genome sequence has been an important goal to allow marker development for restoration and management. Using deep-coverage Illumina and Oxford Nanopore sequencing, combined with Dovetail chromosome conformation capture libraries, the genome was assembled into eleven chromosome-scale scaffolds containing 8.125 Gbp of sequence. Iso-Seq transcripts, assembled from three distinct tissues, was used as evidence to annotate a total of 41,632 protein-coding genes. The genome was found to contain, distributed unevenly across all 11 chromosomes and in 63 orthogroups, over 900 complete or partial predicted NLR genes, of which 375 are supported by annotation derived from protein evidence and gene modeling. This giant sequoia reference genome sequence represents the first genome sequenced in the Cupressaceae family, and lays a foundation for using genomic tools to aid in giant sequoia conservation and management.
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Perry A, Wachowiak W, Downing A, Talbot R, Cavers S. Development of a single nucleotide polymorphism array for population genomic studies in four European pine species. Mol Ecol Resour 2020; 20:1697-1705. [PMID: 32633888 DOI: 10.1111/1755-0998.13223] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/03/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Pines are some of the most ecologically and economically important tree species in the world, and many have enormous natural distributions or have been extensively planted. However, a lack of rapid genotyping capability is hampering progress in understanding the molecular basis of genetic variation in these species. Here, we deliver an efficient tool for genotyping thousands of single nucleotide polymorphism (SNP) markers across the genome that can be applied to genetic studies in pines. Polymorphisms from resequenced candidate genes and transcriptome sequences of P. sylvestris, P. mugo, P. uncinata, P. uliginosa and P. radiata were used to design a 49,829 SNP array (Axiom_PineGAP, Thermo Fisher). Over a third (34.68%) of the unigenes identified from the P. sylvestris transcriptome were represented on the array, which was used to screen samples of four pine species. The conversion rate for the array on all samples was 42% (N = 20,795 SNPs) and was similar for SNPs sourced from resequenced candidate gene and transcriptome sequences. The broad representation of gene ontology terms by unigenes containing converted SNPs reflected their coverage across the full transcriptome. Over a quarter of successfully converted SNPs were polymorphic among all species, and the data were successful in discriminating among the species and some individual populations. The SNP array provides a valuable new tool to advance genetic studies in these species and demonstrates the effectiveness of the technology for rapid genotyping in species with large and complex genomes.
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Affiliation(s)
- Annika Perry
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
| | - Witold Wachowiak
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Alison Downing
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Richard Talbot
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Stephen Cavers
- UK Centre for Ecology & Hydrology Edinburgh, Penicuik, UK
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Dort EN, Tanguay P, Hamelin RC. CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology. FRONTIERS IN PLANT SCIENCE 2020; 11:1126. [PMID: 32793272 PMCID: PMC7387688 DOI: 10.3389/fpls.2020.01126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/08/2020] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas9 gene editing technology has taken the scientific community by storm since its development in 2012. First discovered in 1987, CRISPR/Cas systems act as an adaptive immune response in archaea and bacteria that defends against invading bacteriophages and plasmids. CRISPR/Cas9 gene editing technology modifies this immune response to function in eukaryotic cells as a highly specific, RNA-guided complex that can edit almost any genetic target. This technology has applications in all biological fields, including plant pathology. However, examples of its use in forest pathology are essentially nonexistent. The aim of this review is to give researchers a deeper understanding of the native CRISPR/Cas systems and how they were adapted into the CRISPR/Cas9 technology used today in plant pathology-this information is crucial for researchers aiming to use this technology in the pathosystems they study. We review the current applications of CRISPR/Cas9 in plant pathology and propose future directions for research in forest pathosystems where this technology is currently underutilized.
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Affiliation(s)
- Erika N. Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada
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40
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The plastid NAD(P)H dehydrogenase-like complex: structure, function and evolutionary dynamics. Biochem J 2020; 476:2743-2756. [PMID: 31654059 DOI: 10.1042/bcj20190365] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 11/17/2022]
Abstract
The thylakoid NAD(P)H dehydrogenase-like (NDH) complex is a large protein complex that reduces plastoquinone and pumps protons into the lumen generating protonmotive force. In plants, the complex consists of both nuclear and chloroplast-encoded subunits. Despite its perceived importance for stress tolerance and ATP generation, chloroplast-encoded NDH subunits have been lost numerous times during evolution in species occupying seemingly unrelated environmental niches. We have generated a phylogenetic tree that reveals independent losses in multiple phylogenetic lineages, and we use this tree as a reference to discuss possible evolutionary contexts that may have relaxed selective pressure for retention of ndh genes. While we are still yet unable to pinpoint a singular specific lifestyle that negates the need for NDH, we are able to rule out several long-standing explanations. In light of this, we discuss the biochemical changes that would be required for the chloroplast to dispense with NDH functionality with regards to known and proposed NDH-related reactions.
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Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution. Curr Biol 2020; 30:1783-1800.e11. [DOI: 10.1016/j.cub.2020.02.086] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/04/2020] [Accepted: 02/27/2020] [Indexed: 12/31/2022]
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Howe GT, Jayawickrama K, Kolpak SE, Kling J, Trappe M, Hipkins V, Ye T, Guida S, Cronn R, Cushman SA, McEvoy S. An Axiom SNP genotyping array for Douglas-fir. BMC Genomics 2020; 21:9. [PMID: 31900111 PMCID: PMC6942338 DOI: 10.1186/s12864-019-6383-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In forest trees, genetic markers have been used to understand the genetic architecture of natural populations, identify quantitative trait loci, infer gene function, and enhance tree breeding. Recently, new, efficient technologies for genotyping thousands to millions of single nucleotide polymorphisms (SNPs) have finally made large-scale use of genetic markers widely available. These methods will be exceedingly valuable for improving tree breeding and understanding the ecological genetics of Douglas-fir, one of the most economically and ecologically important trees in the world. RESULTS We designed SNP assays for 55,766 potential SNPs that were discovered from previous transcriptome sequencing projects. We tested the array on ~ 2300 related and unrelated coastal Douglas-fir trees (Pseudotsuga menziesii var. menziesii) from Oregon and Washington, and 13 trees of interior Douglas-fir (P. menziesii var. glauca). As many as ~ 28 K SNPs were reliably genotyped and polymorphic, depending on the selected SNP call rate. To increase the number of SNPs and improve genome coverage, we developed protocols to 'rescue' SNPs that did not pass the default Affymetrix quality control criteria (e.g., 97% SNP call rate). Lowering the SNP call rate threshold from 97 to 60% increased the number of successful SNPs from 20,669 to 28,094. We used a subset of 395 unrelated trees to calculate SNP population genetic statistics for coastal Douglas-fir. Over a range of call rate thresholds (97 to 60%), the median call rate for SNPs in Hardy-Weinberg equilibrium ranged from 99.2 to 99.7%, and the median minor allele frequency ranged from 0.198 to 0.233. The successful SNPs also worked well on interior Douglas-fir. CONCLUSIONS Based on the original transcriptome assemblies and comparisons to version 1.0 of the Douglas-fir reference genome, we conclude that these SNPs can be used to genotype about 10 K to 15 K loci. The Axiom genotyping array will serve as an excellent foundation for studying the population genomics of Douglas-fir and for implementing genomic selection. We are currently using the array to construct a linkage map and test genomic selection in a three-generation breeding program for coastal Douglas-fir.
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Affiliation(s)
- Glenn T Howe
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA.
| | - Keith Jayawickrama
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Scott E Kolpak
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Jennifer Kling
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Matt Trappe
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Valerie Hipkins
- USDA Forest Service, National Forest Genetics Laboratory, Placerville, CA, USA
| | - Terrance Ye
- Northwest Tree Improvement Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | | | - Richard Cronn
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA
| | - Samuel A Cushman
- USDA Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Susan McEvoy
- Pacific Northwest Tree Improvement Research Cooperative, Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
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43
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Variant Calling Using Whole Genome Resequencing and Sequence Capture for Population and Evolutionary Genomic Inferences in Norway Spruce (Picea Abies). COMPENDIUM OF PLANT GENOMES 2020. [DOI: 10.1007/978-3-030-21001-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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44
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Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). G3-GENES GENOMES GENETICS 2019; 9:3663-3672. [PMID: 31506321 PMCID: PMC6829139 DOI: 10.1534/g3.119.400684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.
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A Complete Transcriptional Landscape Analysis of Pinus elliottii Engelm. Using Third-Generation Sequencing and Comparative Analysis in the Pinus Phylogeny. FORESTS 2019. [DOI: 10.3390/f10110942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The planting of Pinus elliottii Engelm. has now reached close to three million ha in China. Molecular breeding as part of the improvement program for P. elliottii in southern China has been carried out in recent years. Third-generation sequencing (Pacbio sequencing technology, TGS) was used to obtain the exome of P. elliottii for molecular breeding. A total of 35.8 Gb clean reads were generated using TGS. After removing the redundant reads, we obtained 80,339 high-accuracy transcripts. Significantly, a total of 76,411 transcripts (95.1%) were blasted to public annotation databases. We predicted 65,062 intact coding sequences (CDSs), 8916 alternative splicing events, 1937 long non-coding RNAs, and 22,109 simple sequence repeats (SSRs) based on these obtained transcripts. Using the public databases and the data obtained above, 23 orthologous single-copy genes were identified to analyze the phylogenetic relationships for Pinus firstly including P. elliottii. Many positive selection genes involved in important biological processes and metabolism pathways were identified between P. elliottii and other pines. These positive selection genes could be candidate genes to be researched on the genetic basis of superior performance. Our study is the first to reveal the full-length and well-annotated transcripts of P. elliottii, which could provide reference for short transcriptome sequences in the research of genetics, phylogenetics, and genetic improvement for the non-reference genome species.
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Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019; 9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
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Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M, Fussi B, Gömöry D, González-Martínez SC, Grivet D, Gut M, Hansen OK, Heer K, Kaya Z, Krutovsky KV, Kersten B, Liepelt S, Opgenoorth L, Sperisen C, Ullrich KK, Vendramin GG, Westergren M, Ziegenhagen B, Alioto T, Gugerli F, Heinze B, Höhn M, Troggio M, Neale DB. A Reference Genome Sequence for the European Silver Fir ( Abies alba Mill.): A Community-Generated Genomic Resource. G3 (BETHESDA, MD.) 2019; 9:2039-2049. [PMID: 31217262 PMCID: PMC6643874 DOI: 10.1534/g3.119.400083] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/11/2019] [Indexed: 02/08/2023]
Abstract
Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will open the gate for new research and more precise genetic monitoring of European silver fir forests.
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Affiliation(s)
- Elena Mosca
- C3A - Centro Agricoltura Alimenti Ambiente, University of Trento, via E. Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
| | - Luca Bianco
- Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - Christian Rellstab
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Sabine Brodbeck
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Katalin Csilléry
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- University of Zürich, Department of Evolutionary Biology and Environmental Studies, Winterthurerstrasse 190, CH-8057 Zurich
| | - Bruno Fady
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche Ecologie des Forêts Méditerranéennes (URFM), Site Agroparc, Domaine Saint Paul, 84914 Avignon, France
| | - Matthias Fladung
- Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany
| | - Barbara Fussi
- Bavarian Office for Forest Seeding and Planting (ASP), Applied Forest Genetics, Forstamtsplatz 1, 83317 Teisendorf, Germany
| | - Dušan Gömöry
- Technical University in Zvolen, TG Masaryka 24, 96053 Zvolen, Slovakia
| | - Santiago C González-Martínez
- Institut National de la Recherche Agronomique (INRA), UMR1202 Biodiversity, Genes & Communities (BIOGECO), University of Bordeaux, 69, route d'Arcachon, 33610 Cestas, France
| | - Delphine Grivet
- INIA Forest Research Centre, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Ole Kim Hansen
- Department of Geosciences and Natural Resource Management (IGN), University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Katrin Heer
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Zeki Kaya
- Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey
| | - Konstantin V Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
- Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str. 3, 11991 Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 50a/2 Akademgorodok, 660036 Krasnoyarsk, Russia
| | - Birgit Kersten
- Thünen-Institute of Forest Genetics, Sieker Landstr, 2, 22927 Grosshansdorf, Germany
| | - Sascha Liepelt
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Lars Opgenoorth
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Christoph Sperisen
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Kristian K Ullrich
- Department of Biological Sciences (METU), Middle East Technical University, 06800 Çankaya/Ankara, Turkey
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources, National Research Council, Via Madonna del Piano 10,50019 Sesto Fiorentino (Firenze), Italy
| | - Marjana Westergren
- Slovenian Forestry Institute (SFI), Gozdarskiinštitut Slovenije), Večna pot 2, 1000 Ljubljana, Slovenia
| | - Birgit Ziegenhagen
- Philipps-Universität Marburg, Faculty of Biology (PUM), Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, BaldiriReixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Felix Gugerli
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Berthold Heinze
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent Weg 8, 1130 Wien, Austria
| | - Maria Höhn
- Max Planck Institute for Evolutionary Biology, Department for Evolutionary Genetics (MPI), August Thienemann Str. 2, 24306 Ploen, Germany
| | - Michela Troggio
- Fondazione Edmund Mach, Via Mach 1, 38010 S. Michele a/Adige (TN), Italy
| | - David B Neale
- Department of Plant Sciences, University of California at Davis (UCD), Davis 95616
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Grebe S, Trotta A, Bajwa AA, Suorsa M, Gollan PJ, Jansson S, Tikkanen M, Aro EM. The unique photosynthetic apparatus of Pinaceae: analysis of photosynthetic complexes in Picea abies. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3211-3225. [PMID: 30938447 PMCID: PMC6598058 DOI: 10.1093/jxb/erz127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/13/2019] [Indexed: 05/07/2023]
Abstract
Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.
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Affiliation(s)
- Steffen Grebe
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Andrea Trotta
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Azfar A Bajwa
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Marjaana Suorsa
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Peter J Gollan
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Stefan Jansson
- Umeå University, Faculty of Science and Technology, Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå, Sweden
| | - Mikko Tikkanen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
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Thistlethwaite FR, Ratcliffe B, Klápště J, Porth I, Chen C, Stoehr MU, El-Kassaby YA. Genomic selection of juvenile height across a single-generational gap in Douglas-fir. Heredity (Edinb) 2019; 122:848-863. [PMID: 30631145 PMCID: PMC6781123 DOI: 10.1038/s41437-018-0172-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 11/30/2022] Open
Abstract
Here, we perform cross-generational GS analysis on coastal Douglas-fir (Pseudotsuga menziesii), reflecting trans-generational selective breeding application. A total of 1321 trees, representing 37 full-sib F1 families from 3 environments in British Columbia, Canada, were used as the training population for (1) EBVs (estimated breeding values) of juvenile height (HTJ) in the F1 generation predicting genomic EBVs of HTJ of 136 individuals in the F2 generation, (2) deregressed EBVs of F1 HTJ predicting deregressed genomic EBVs of F2 HTJ, (3) F1 mature height (HT35) predicting HTJ EBVs in F2, and (4) deregressed F1 HT35 predicting genomic deregressed HTJ EBVs in F2. Ridge regression best linear unbiased predictor (RR-BLUP), generalized ridge regression (GRR), and Bayes-B GS methods were used and compared to pedigree-based (ABLUP) predictions. GS accuracies for scenarios 1 (0.92, 0.91, and 0.91) and 3 (0.57, 0.56, and 0.58) were similar to their ABLUP counterparts (0.92 and 0.60, respectively) (using RR-BLUP, GRR, and Bayes-B). Results using deregressed values fell dramatically for both scenarios 2 and 4 which approached zero in many cases. Cross-generational GS validation of juvenile height in Douglas-fir produced predictive accuracies almost as high as that of ABLUP. Without capturing LD, GS cannot surpass the prediction of ABLUP. Here we tracked pedigree relatedness between training and validation sets. More markers or improved distribution of markers are required to capture LD in Douglas-fir. This is essential for accurate forward selection among siblings as markers that track pedigree are of little use for forward selection of individuals within controlled pollinated families.
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Affiliation(s)
- Frances R Thistlethwaite
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3046, New Zealand
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Praha 6, 165 21, Czech Republic
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, G1V 0A6, Québec, QC, Canada
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078-3035, USA
| | - Michael U Stoehr
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
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50
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Gautier F, Label P, Eliášová K, Leplé JC, Motyka V, Boizot N, Vondráková Z, Malbeck J, Trávníčková A, Le Metté C, Lesage-Descauses MC, Lomenech AM, Trontin JF, Costa G, Lelu-Walter MA, Teyssier C. Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir ( Pseudotsuga menziesii [Mirb.]). FRONTIERS IN PLANT SCIENCE 2019; 10:118. [PMID: 30873184 PMCID: PMC6403139 DOI: 10.3389/fpls.2019.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/23/2019] [Indexed: 05/08/2023]
Abstract
Somatic embryogenesis techniques have been developed for most coniferous species, but only using very juvenile material. To extend the techniques' scope, better integrated understanding of the key biological, physiological and molecular characteristics of embryogenic state is required. Therefore, embryonal masses (EMs) and non-embryogenic calli (NECs) have been compared during proliferation at multiple levels. EMs and NECs originating from a single somatic embryo (isogenic lines) of each of three unrelated genotypes were used in the analyses, which included comparison of the lines' anatomy by transmission light microscopy, transcriptomes by RNAseq Illumina sequencing, proteomes by free-gel analysis, contents of endogenous phytohormones (indole-3-acetic acid, cytokinins and ABA) by LC-MS analysis, and soluble sugar contents by HPLC. EMs were characterized by upregulation (relative to levels in NECs) of transcripts, proteins, transcription factors and active cytokinins associated with cell differentiation accompanied by histological, carbohydrate content and genetic markers of cell division. In contrast, NECs were characterized by upregulation (relative to levels in EMs) of transcripts, proteins and products associated with responses to stimuli (ABA, degradation forms of cytokinins, phenols), oxidative stress (reactive oxygen species) and carbohydrate storage (starch). Sub-Network Enrichment Analyses that highlighted functions and interactions of transcripts and proteins that significantly differed between EMs and NECs corroborated these findings. The study shows the utility of a novel approach involving integrated multi-scale transcriptomic, proteomic, biochemical, histological and anatomical analyses to obtain insights into molecular events associated with embryogenesis and more specifically to the embryogenic state of cell in Douglas-fir.
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Affiliation(s)
- Florian Gautier
- BioForA, INRA, ONF, Orléans, France
- PEIRENE, Sylva LIM, Université de Limoges, Limoges, France
| | | | - Kateřina Eliášová
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Václav Motyka
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | - Zuzana Vondráková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Jiří Malbeck
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | - Alena Trávníčková
- Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czechia
| | | | | | - Anne-Marie Lomenech
- Centre de Génomique Fonctionnelle, Plateforme Protéome, University of Bordeaux, Bordeaux, France
| | | | - Guy Costa
- PEIRENE, Sylva LIM, Université de Limoges, Limoges, France
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