101
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Hu YN, Zhao L, Buggs RJA, Zhang XM, Li J, Wang N. Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage. ANNALS OF BOTANY 2019; 123:1179-1189. [PMID: 30916314 PMCID: PMC6612935 DOI: 10.1093/aob/mcz024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/15/2019] [Accepted: 02/05/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Differences in local abundance and ploidy level are predicted to impact the direction of introgression between species. Here, we tested these hypotheses on populations of Betula albosinensis (red birch) and Betula platyphylla (white birch) which were thought to differ in ploidy level, the former being tetraploid and the latter diploid. METHODS We sampled 391 birch individuals from nine localities in China, and classified them into species based on leaf morphology. Twelve nuclear microsatellite markers were genotyped in each sample, and analysed using principal coordinates analysis and STRUCTURE software. We compared the effects of two different methods of scoring polyploid genotypes on population genetic analyses. We analysed the effect of ploidy, local species abundance and latitude on levels of introgression between the species. KEY RESULTS Leaf morphology divided our samples into red and white birch, but genetic analyses unexpectedly revealed two groups within red birch, one of which was tetraploid, as expected, but the other of which appeared to have diploid microsatellite genotypes. Five individuals were identified as early-generation hybrids or backcrosses between white birch and red birch and five were identified between red birch and 'diploid' red birch. Cline analysis showed that levels of admixture were not significantly correlated with latitude. Estimated genetic differentiation among species was not significantly different between determined tetraploid and undetermined tetraploid genotypes. CONCLUSIONS Limited hybridization and gene flow have occurred between red birch and white birch. Relative species abundance and ploidy level do not impact the direction of introgression between them, as genetic admixture is roughly symmetrical. We unexpectedly found populations of apparently diploid red birch and this taxon may be a progenitor of allotetraploid red birch populations. Incomplete lineage sorting may explain patterns of genetic admixture between apparently diploid and allotetraploid red birch.
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Affiliation(s)
- Ya-Nan Hu
- College of Forestry, Shandong Agricultural University, Tai’an city, Shandong province, China
| | - Lei Zhao
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Richard J A Buggs
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Xue-Min Zhang
- Mulan-Weichang National Forestry Administration, Chengde, China
| | - Jun Li
- Mulan-Weichang National Forestry Administration, Chengde, China
| | - Nian Wang
- College of Forestry, Shandong Agricultural University, Tai’an city, Shandong province, China
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Guo L, Liang S, Zhang Z, Liu H, Wang S, Pan K, Xu J, Ren X, Pei S, Yang G. Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation. Commun Biol 2019; 2:249. [PMID: 31286066 PMCID: PMC6610115 DOI: 10.1038/s42003-019-0500-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
The species of the genus Nannochloropsis are unique in their maintenance of a nucleus-plastid continuum throughout their cell cycle, non-motility and asexual reproduction. These characteristics should have been endorsed in their gene assemblages (genomes). Here we show that N. oceanica has a genome of 29.3 Mb consisting of 32 pseudochromosomes and containing 7,330 protein-coding genes; and the host nucleus may have been overthrown by an ancient red alga symbiont nucleus during speciation through secondary endosymbiosis. In addition, N. oceanica has lost its flagella and abilities to undergo meiosis and sexual reproduction, and adopted a genome reduction strategy during speciation. We propose that N. oceanica emerged through the active fusion of a host protist and a photosynthesizing ancient red alga and the symbiont nucleus became dominant over the host nucleus while the chloroplast was wrapped by two layers of endoplasmic reticulum. Our findings evidenced an alternative speciation pathway of eukaryotes.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Sijie Liang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Zhongyi Zhang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Hang Liu
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Songwen Wang
- College of Agriculture and Resources and Environment, Tianjin Agricultural University, Tianjin, 300384 P. R. China
| | - Kehou Pan
- Laboratory of Applied Microalgae, College of Fisheries, OUC, Qingdao, 266003 P. R. China
| | - Jian Xu
- Functional Genomics Group, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 P. R. China
| | - Xue Ren
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 100176 P. R. China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 100176 P. R. China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
- Institutes of Evolution and Marine Biodiversity, OUC, Qingdao, 266003 P. R. China
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, OUC, Qingdao, 266003 P. R. China
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103
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Gang H, Li R, Zhao Y, Liu G, Chen S, Jiang J. Loss of GLK1 transcription factor function reveals new insights in chlorophyll biosynthesis and chloroplast development. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3125-3138. [PMID: 30921458 DOI: 10.1093/jxb/erz128] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/06/2019] [Indexed: 05/14/2023]
Abstract
Birch (Betula platyphylla × B. pendula) is an important tree for landscaping due to its attractive white bark and straight trunk. In this study, we characterized a T-DNA yellow-green leaf mutant, yl. We identified six insertion sites (ISs) in the mutant by genome resequencing and found a 40-kb deletion containing BpGLK1 around IS2 on chromosome 2. Complementation experiments with the yl mutant and repression of BpGLK1 in wild-type plants confirmed that BpGLK1 was responsible for the mutated phenotype. Physiological and ultrastructural analyses showed that the leaves of the yl mutant and BpGLK1-repression lines had decreased chlorophyll content and defective chloroplast development compared to the wild-type. Furthermore, the loss function of BpGLK1 also affected photosynthesis in leaves. Transcriptomics, proteomics, and ChIP-PCR analysis revealed that BpGLK1 directly interacted with the promoter of genes related to antenna proteins, chlorophyll biosynthesis, and photosystem subunit synthesis, and regulated their expression. Overall, our research not only provides new insights into the mechanism of chloroplast development and chlorophyll biosynthesis regulated by BpGLK1, but also provides new transgenic birch varieties with various levels of yellowing leaves by repressing BpGLK1 expression.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ranhong Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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104
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Alonso-Serra J, Safronov O, Lim KJ, Fraser-Miller SJ, Blokhina OB, Campilho A, Chong SL, Fagerstedt K, Haavikko R, Helariutta Y, Immanen J, Kangasjärvi J, Kauppila TJ, Lehtonen M, Ragni L, Rajaraman S, Räsänen RM, Safdari P, Tenkanen M, Yli-Kauhaluoma JT, Teeri TH, Strachan CJ, Nieminen K, Salojärvi J. Tissue-specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark. THE NEW PHYTOLOGIST 2019; 222:1816-1831. [PMID: 30724367 DOI: 10.1111/nph.15725] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/25/2019] [Indexed: 05/09/2023]
Abstract
Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem-environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch (Betula pendula) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter- and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue-specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small-scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.
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Affiliation(s)
- Juan Alonso-Serra
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Kean-Jin Lim
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Sara J Fraser-Miller
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
- The Dodd-Walls Centre for Photonic and Quantum Technologies, Department of Chemistry, University of Otago, 9054, Dunedin, New Zealand
| | - Olga B Blokhina
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Ana Campilho
- Research Center in Biodiversity and Genetic Resources, Department of Biology, Faculty of Sciences, University of Porto, 4485-661, Porto, Portugal
| | - Sun-Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
- Department of Food and Nutrition, University of Helsinki, 00014, Helsinki, Finland
| | - Kurt Fagerstedt
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Raisa Haavikko
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Ykä Helariutta
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Juha Immanen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Natural Resources Institute Finland (Luke), 00710, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Tiina J Kauppila
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Mari Lehtonen
- Laboratory Center, Finnish Environment Institute (SYKE), 00790, Helsinki, Finland
| | - Laura Ragni
- ZMBP-Center for Plant Molecular Biology, University of Tübingen, D-72076, Tübingen, Germany
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Riikka-Marjaana Räsänen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Pezhman Safdari
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Maija Tenkanen
- Department of Food and Nutrition, University of Helsinki, 00014, Helsinki, Finland
| | - Jari T Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Teemu H Teeri
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, 00014, Helsinki, Finland
| | - Clare J Strachan
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Kaisa Nieminen
- Natural Resources Institute Finland (Luke), 00710, Helsinki, Finland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore, Singapore
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105
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Galibina NA, Novitskaya LL, Nikerova KM, Moshchenskaya YL, Borodina MN, Sofronova IN. Apoplastic Invertase Activity Regulation in the Cambial Zone of Karelian Birch. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360419010028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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106
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Huang Y, Xiao L, Zhang Z, Zhang R, Wang Z, Huang C, Huang R, Luan Y, Fan T, Wang J, Shen C, Zhang S, Wang X, Randall J, Zheng B, Wu J, Zhang Q, Xia G, Xu C, Chen M, Zhang L, Jiang W, Gao L, Chen Z, Leslie CA, Grauke LJ, Huang J. The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. Gigascience 2019; 8:giz036. [PMID: 31049561 PMCID: PMC6497033 DOI: 10.1093/gigascience/giz036] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/15/2018] [Accepted: 03/19/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits. RESULTS We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar ("Pawnee") and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives. CONCLUSIONS Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.
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Affiliation(s)
- Youjun Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, No. 38 Xueqing Rd., Haidian District, Beijing 100083, China
| | - Rui Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Chunying Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Ren Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Yumeng Luan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Tongqiang Fan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Chen Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Shenmei Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Xinwang Wang
- Pecan Breeding and Genetics, Agricultural Research Service, United States Department of Agriculture, 10200 FM 50, Somerville, TX 77979, USA
| | - Jennifer Randall
- College of Agricultural, Consumer, and Environmental Sciences, New Mexico State University, 3BE Skeen Hall, Las Cruces, NM 88003, USA
| | - Bingsong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Qixiang Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Chuanmei Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
| | - Ming Chen
- School of Life Science, Zhejiang University, No. 866 Yuhangtang Rd., Hangzhou 310058, China
| | - Liangsheng Zhang
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Rd., Cangshan District, Fuzhou 350002, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, No. 38 Xueqing Rd., Haidian District, Beijing 100083, China
| | - Lizhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, No. 132 Lanhei Rd., Kunming 650201, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, No. 20 Nanxincun, Xiangshan Rd., Beijing 100093, China
| | - Charles A Leslie
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - L J Grauke
- Pecan Breeding and Genetics, Agricultural Research Service, United States Department of Agriculture, 10200 FM 50, Somerville, TX 77979, USA
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China
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107
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He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 2019; 51:896-904. [PMID: 31043759 DOI: 10.1038/s41588-019-0382-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.
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Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | | | - Pippa Kay
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Krystalee Wiebe
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - John P Davies
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - Steve R Webb
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ben Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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108
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Gang H, Liu G, Zhang M, Zhao Y, Jiang J, Chen S. Comprehensive characterization of T-DNA integration induced chromosomal rearrangement in a birch T-DNA mutant. BMC Genomics 2019; 20:311. [PMID: 31014254 PMCID: PMC6480916 DOI: 10.1186/s12864-019-5636-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/24/2019] [Indexed: 11/29/2022] Open
Abstract
Background Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA fragments caused chromosomal translocation and deletion in a birch (Betula platyphylla × B. pendula) T-DNA mutant yl. Results We performed PacBio genome resequencing for yl and the result revealed that two ends of a T-DNA can be integrated into plant genome independently because the two ends can be linked to different chromosomes and cause chromosomal translocation. We also found that these T-DNA were connected into tandem fragment regardless of direction before integrating into plant genome. In addition, the integration of T-DNA in yl genome also caused several chromosomal fragments deletion. We then summarized three cases for T-DNA integration model in the yl genome. (1) A T-DNA fragment is linked to the two ends of a double-stranded break (DSB); (2) Only one end of a T-DNA fragment is linked to a DSB; (3) A T-DNA fragment is linked to the ends of different DSBs. All the observations in the yl genome supported the DSB repair model. Conclusions In this study, we showed a comprehensive genome analysis of a T-DNA mutant and provide a new insight into T-DNA integration in plants. These findings would be helpful for the analysis of T-DNA mutants with special phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5636-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huixin Gang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Manman Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yuming Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Walve R, Rastas P, Salmela L. Kermit: linkage map guided long read assembly. Algorithms Mol Biol 2019; 14:8. [PMID: 30930956 PMCID: PMC6425630 DOI: 10.1186/s13015-019-0143-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes. RESULTS We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly. CONCLUSIONS We present the first method to integrate linkage maps directly into genome assembly. With a modest increase in runtime, our method improves contiguity and correctness of genome assembly.
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Affiliation(s)
- Riku Walve
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leena Salmela
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
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110
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Van Cleemput J, Poelaert KCK, Laval K, Impens F, Van den Broeck W, Gevaert K, Nauwynck HJ. Pollens destroy respiratory epithelial cell anchors and drive alphaherpesvirus infection. Sci Rep 2019; 9:4787. [PMID: 30886217 PMCID: PMC6423322 DOI: 10.1038/s41598-019-41305-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Pollens are well-known triggers of respiratory allergies and asthma. The pollen burden in today's ambient air is constantly increasing due to rising climate change and air pollution. How pollens interact with the respiratory mucosa remains largely unknown due to a lack of representative model systems. We here demonstrate how pollen proteases of Kentucky bluegrass, white birch and hazel selectively destroy integrity and anchorage of columnar respiratory epithelial cells, but not of basal cells, in both ex vivo respiratory mucosal explants and in vitro primary equine respiratory epithelial cells (EREC). In turn, this pollen protease-induced damage to respiratory epithelial cell anchorage resulted in increased infection by the host-specific and ancestral alphaherpesvirus equine herpesvirus type 1 (EHV1). Pollen proteases of all three plant species were characterized by zymography and those of white birch were fully identified for the first time as serine proteases of the subtilase family and meiotic prophase aminopeptidase 1 using mass spectrometry-based proteomics. Together, our findings demonstrate that pollen proteases selectively and irreversibly damage integrity and anchorage of columnar respiratory epithelial cells. In turn, alphaherpesviruses benefit from this partial loss-of-barrier function, resulting in increased infection of the respiratory epithelium.
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Affiliation(s)
- Jolien Van Cleemput
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, 08544, USA
| | - Katrien C K Poelaert
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Kathlyn Laval
- Department of Molecular Biology, Princeton University, 119 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey, 08544, USA
| | - Francis Impens
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- VIB Proteomics Core, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Wim Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium
| | - Hans J Nauwynck
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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111
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Vaattovaara A, Leppälä J, Salojärvi J, Wrzaczek M. High-throughput sequencing data and the impact of plant gene annotation quality. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1069-1076. [PMID: 30590678 PMCID: PMC6382340 DOI: 10.1093/jxb/ery434] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/28/2018] [Indexed: 06/02/2023]
Abstract
The use of draft genomes of different species and re-sequencing of accessions and populations are now common tools for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits, such as those for plant stress tolerance and development. In both cases high-quality gene annotation-the identification of protein-coding regions, gene promoters, and 5'- and 3'-untranslated regions-is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families, and segmentally duplicated genes. In this opinion paper, we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies, and the identification of orthologous genes in plants. Furthermore, we predict that incorporating accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
| | - Johanna Leppälä
- Department of Ecology and Environmental Science, Umeå University, Linnaeus väg 6, Umeå, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), Helsinki, Finland
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Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklová M, Kangasjärvi J, Löytynoja A, Hothorn M, Salojärvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol 2019; 2:56. [PMID: 30775457 PMCID: PMC6368629 DOI: 10.1038/s42003-019-0306-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 01/01/2023] Open
Abstract
Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.
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Affiliation(s)
- Aleksia Vaattovaara
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Benjamin Brandt
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Omid Safronov
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Andres Veidenberg
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Markéta Luklová
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- Present Address: Laboratory of Plant Molecular Biology, Institute of Biophysics AS CR, v.v.i. and CEITEC—Central European Institute of Technology, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5 (POB56), FI-00014 Helsinki, Finland
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Michael Wrzaczek
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, VIPS, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1 (POB65), FI-00014 Helsinki, Finland
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113
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Physiological and Transcriptome Analysis of a Yellow-Green Leaf Mutant in Birch (Betula platyphylla × B. Pendula). FORESTS 2019. [DOI: 10.3390/f10020120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chlorophyll (Chl)-deficient mutants are ideal materials for the study of Chl biosynthesis, chloroplast development, and photosynthesis. Although the genes encoding key enzymes related to Chl biosynthesis have been well-characterized in herbaceous plants, rice (Oryza sativa L.), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays L.), yellow-green leaf mutants have not yet been fully studied in tree species. In this work, we explored the molecular mechanism of the leaf color formation in a yellow-green leaf mutant (yl). We investigated the differentially expressed genes (DEGs) between yl and control plants (wild type birch (WT) and BpCCR1 overexpression line 11, (C11)) by transcriptome sequencing. Approximately 1163 genes (874 down-regulated and 289 up-regulated) and 930 genes (755 down-regulated and 175 up-regulated) were found to be differentially expressed in yl compared with WT and C11, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs revealed that photosynthesis antenna proteins represent the most significant enriched pathway. The expressions of photosynthesis antenna proteins are crucial to the leaf color formation in yl. We also found that Chl accumulate, leaf anatomical structure, photosynthesis, and growth were affected in yl. Taken together, our results not only provide the difference of phenomenal, physiological, and gene expression characteristics in leaves between yl mutant and control plants, but also provide a new insight into the mutation underlying the chlorotic leaf phenotype in birch.
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114
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Jia H, Jia H, Cai Q, Wang Y, Zhao H, Yang W, Wang G, Li Y, Zhan D, Shen Y, Niu Q, Chang L, Qiu J, Zhao L, Xie H, Fu W, Jin J, Li X, Jiao Y, Zhou C, Tu T, Chai C, Gao J, Fan L, van de Weg E, Wang J, Gao Z. The red bayberry genome and genetic basis of sex determination. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:397-409. [PMID: 29992702 PMCID: PMC6335074 DOI: 10.1111/pbi.12985] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/01/2018] [Accepted: 07/04/2018] [Indexed: 05/12/2023]
Abstract
Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59-Kb female-specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non-recombinant in the female-specific region. Sex-specific molecular markers developed from candidate genes co-segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.
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Affiliation(s)
- Hui‐Min Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hui‐Juan Jia
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | | | - Yan Wang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hai‐Bo Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wei‐Fei Yang
- Hangzhou 1 Gene LtdHangzhouChina
- Forestry Technology Extension CenterYuyaoNingboChina
- Present address:
Annoroad Gene Tech. Co., LtdBeijingChina
| | - Guo‐Yun Wang
- Forestry Technology Extension CenterYuyaoNingboChina
| | - Ying‐Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | | | - Yu‐Tong Shen
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qing‐Feng Niu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular GeneticsCenter of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | - Le Chang
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jie Qiu
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Lan Zhao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Han‐Bing Xie
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Wan‐Yi Fu
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jing Jin
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Xiong‐Wei Li
- Forest & Fruit Tree InstituteShanghai Academy of Agricultural SciencesShanghaiChina
| | - Yun Jiao
- Institute of ForestryNingbo Academy of Agricultural ScienceNingboChina
| | | | - Ting Tu
- Shunmei Breeding and Propagation Centre for Chinese BayberryYuyaoChina
| | | | | | - Long‐Jiang Fan
- Institute of Crop Science & Institute of BioinformaticsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Eric van de Weg
- Plant Breeding‐Wageningen University and ResearchWageningenThe Netherlands
| | | | - Zhong‐Shan Gao
- Institute of Fruit ScienceCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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115
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Hill JL, Hollender CA. Branching out: new insights into the genetic regulation of shoot architecture in trees. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:73-80. [PMID: 30339931 DOI: 10.1016/j.pbi.2018.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 05/03/2023]
Abstract
Directional growth in all plants involves both phototropic and gravitropic responses. Accordingly, mechanisms controlling shoot architecture throughout the plant kingdom are likely similar. However, as forms vary between species due in part to gene copy number and functional divergence, some aspects of how plants predetermine and regulate architecture can differ. This is especially true when comparing annual herbaceous species (e.g. model plants) to woody perennials such as trees. In the past decade, inexpensive genomic sequencing and technological advances enabled gene discovery and functional analyses in trees. This led to the identification of genes associated with tree shoot architecture control. Here, we present recent discoveries on the regulation of shoot architectures for which causative genes have been identified, including dwarf, weeping, columnar, and pillar growth habits. We also discuss potential applications of these findings.
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Affiliation(s)
- Joseph L Hill
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA.
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116
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Yang Y, Ma T, Wang Z, Lu Z, Li Y, Fu C, Chen X, Zhao M, Olson MS, Liu J. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat Commun 2018; 9:5449. [PMID: 30575743 PMCID: PMC6303402 DOI: 10.1038/s41467-018-07913-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Increased human activity and climate change are driving numerous tree species to endangered status, and in the worst cases extinction. Here we examine the genomic signatures of the critically endangered ironwood tree Ostrya rehderiana and its widespread congener O. chinensis. Both species have similar demographic histories prior to the Last Glacial Maximum (LGM); however, the effective population size of O. rehderiana continued to decrease through the last 10,000 years, whereas O. chinensis recovered to Pre-LGM numbers. O. rehderiana accumulated more deleterious mutations, but purged more severely deleterious recessive variations than in O. chinensis. This purging and the gradually reduced inbreeding depression together may have mitigated extinction and contributed to the possible future survival of the outcrossing O. rehderiana. Our findings provide critical insights into the evolutionary history of population collapse and the potential for future recovery of the endangered trees.
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Affiliation(s)
- Yongzhi Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zefu Wang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China
| | - Chengxin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of Ministry of Education, and College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xiaoyong Chen
- School of Ecological & Environmental Sciences, East China Normal University, Dongchuan Road 500, 200241, Shanghai, China
| | - Mingshui Zhao
- Zhejiang Tianmushan National Nature Reserve Management Bureau, 310058, Hangzhou, China
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, China.
- State Key Laboratory of Grassland Agro-Ecosystem, College of Life Sciences, Lanzhou University, 730000, Lanzhou, China.
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117
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Wang S, Yang C, Zhao X, Chen S, Qu GZ. Complete chloroplast genome sequence of Betula platyphylla: gene organization, RNA editing, and comparative and phylogenetic analyses. BMC Genomics 2018; 19:950. [PMID: 30572840 PMCID: PMC6302522 DOI: 10.1186/s12864-018-5346-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editing and phylogeny. In this study, we sequenced and analyzed the complete chloroplast (cp) genome sequence of B. platyphylla. RESULTS The complete cp genome of B. platyphylla was 160,518 bp in length, which included a pair of inverted repeats (IRs) of 26,056 bp that separated a large single copy (LSC) region of 89,397 bp and a small single copy (SSC) region of 19,009 bp. The annotation contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes and 8 rRNA genes. There were 3 genes using alternative initiation codons. Comparative genomics showed that the sequence of the Fagales species cp genome was relatively conserved, but there were still some high variation regions that could be used as molecular markers. The IR expansion event of B. platyphylla resulted in larger cp genomes and rps19 pseudogene formation. The simple sequence repeat (SSR) analysis showed that there were 105 SSRs in the cp genome of B. platyphylla. RNA editing sites recognition indicated that at least 80 RNA editing events occurred in the cp genome. Most of the substitutions were C to U, while a small proportion of them were not. In particular, three editing loci on the rRNA were converted to more than two other bases that had never been reported. For synonymous conversion, most of them increased the relative synonymous codon usage (RSCU) value of the codons. The phylogenetic analysis suggested that B. platyphylla had a closer evolutionary relationship with B. pendula than B. nana. CONCLUSIONS In this study, we not only obtained and annotated the complete cp genome sequence of B. platyphylla, but we also identified new RNA editing sites and predicted the phylogenetic relationships among Fagales species. These findings will facilitate genomic, genetic engineering and phylogenetic studies of this important species.
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Affiliation(s)
- Sui Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040 China
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118
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Nelson TC, Monnahan PJ, McIntosh MK, Anderson K, MacArthur-Waltz E, Finseth FR, Kelly JK, Fishman L. Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers. Mol Ecol 2018; 28:1460-1475. [PMID: 30346101 DOI: 10.1111/mec.14904] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/03/2018] [Accepted: 10/08/2018] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on a tRNA ligase gene (Migut.N02091; RLG1a) exhibiting unprecedented, and fitness-relevant, CNV within an annual population of the yellow monkeyflower Mimulus guttatus. RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate-frequency three-copy variants of RLG1a (trip+; 5/35 = 14%), and trip+ lines exhibited elevated RLG1a expression under multiple conditions. trip+ carriers, in addition to being over-represented in late-flowering and large-flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rare RLG1a variant (high+) that carries 250-300 copies of RLG1a totalling ~5.7 Mb (20-40% of a chromosome). In the progeny of a high+ carrier, Mendelian segregation of diagnostic alleles and qPCR-based copy counts indicate that high+ is a single tandem array unlinked to the single-copy RLG1a locus. In the wild, high+ carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; both p < 0.01), while single-copy individuals were twice as fecund as either CNV type in a lush year (2016: p < 0.005). Our results demonstrate fluctuating selection on CNVs affecting phenological traits in a wild population, suggest that plant tRNA ligases mediate stress-responsive life-history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Patrick J Monnahan
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Mariah K McIntosh
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Kayli Anderson
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | | | - Findley R Finseth
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - John K Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana
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Complex Haplotypes of GSTM1 Gene Deletions Harbor Signatures of a Selective Sweep in East Asian Populations. G3-GENES GENOMES GENETICS 2018; 8:2953-2966. [PMID: 30061374 PMCID: PMC6118300 DOI: 10.1534/g3.118.200462] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The deletion of the metabolizing Glutathione S-transferase Mu 1 (GSTM1) gene has been associated with multiple cancers, metabolic and autoimmune disorders, as well as drug response. It is unusually common, with allele frequency reaching up to 75% in some human populations. Such high allele frequency of a derived allele with apparent impact on an otherwise conserved gene is a rare phenomenon. To investigate the evolutionary history of this locus, we analyzed 310 genomes using population genetics tools. Our analysis revealed a surprising lack of linkage disequilibrium between the deletion and the flanking single nucleotide variants in this locus. Tests that measure extended homozygosity and rapid change in allele frequency revealed signatures of an incomplete sweep in the locus. Using empirical approaches, we identified the Tanuki haplogroup, which carries the GSTM1 deletion and is found in approximately 70% of East Asian chromosomes. This haplogroup has rapidly increased in frequency in East Asian populations, contributing to a high population differentiation among continental human groups. We showed that extended homozygosity and population differentiation for this haplogroup is incompatible with simulated neutral expectations in East Asian populations. In parallel, we found that the Tanuki haplogroup is significantly associated with the expression levels of other GSTM genes. Collectively, our results suggest that standing variation in this locus has likely undergone an incomplete sweep in East Asia with regulatory impact on multiple GSTM genes. Our study provides the necessary framework for further studies to elucidate the evolutionary reasons that maintain disease-susceptibility variants in the GSTM1 locus.
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120
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Somervuo P, Koskinen P, Mei P, Holm L, Auvinen P, Paulin L. BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. BMC Bioinformatics 2018; 19:257. [PMID: 29976145 PMCID: PMC6034344 DOI: 10.1186/s12859-018-2262-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection. RESULTS We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel . CONCLUSIONS Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.
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Affiliation(s)
- Panu Somervuo
- Mathematical Biology Group, Department of Biosciences, FIN-00014 University of Helsinki, P.O.Box 65 Finland
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Patrik Koskinen
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Peng Mei
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Liisa Holm
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
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121
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Oksanen E. Trichomes form an important first line of defence against adverse environment-New evidence for ozone stress mitigation. PLANT, CELL & ENVIRONMENT 2018; 41:1497-1499. [PMID: 29508922 DOI: 10.1111/pce.13187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/03/2023]
Affiliation(s)
- Elina Oksanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101, Joensuu, Finland
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122
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Maas DL, Prost S, Bi K, Smith LL, Armstrong EE, Aji LP, Toha AHA, Gillespie RG, Becking LE. Rapid divergence of mussel populations despite incomplete barriers to dispersal. Mol Ecol 2018; 27:1556-1571. [DOI: 10.1111/mec.14556] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/25/2018] [Accepted: 02/26/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Diede L. Maas
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
| | - Stefan Prost
- Department of Biology; Stanford University; Stanford CA USA
- Department of Integrative Biology; Center for Theoretical Evolutionary Genomics; University of California; Berkeley CA USA
| | - Ke Bi
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
- Computational Genomics Resource Laboratory; California Institute for Quantitative Biosciences; University of California; Berkley CA USA
| | - Lydia L. Smith
- Museum of Vertebrate Zoology; University of California; Berkeley CA USA
| | | | - Ludi P. Aji
- Research Centre for Oceanography; Indonesian Institute of Sciences; Jakarta Indonesia
| | | | - Rosemary G. Gillespie
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
| | - Leontine E. Becking
- Department of Marine Animal Ecology; Wageningen University & Research; Wageningen The Netherlands
- Department of Environmental Science, Policy, and Management; University of California; Berkeley CA USA
- Wageningen Marine Research; Den Helder The Netherlands
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123
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Hodel RG, Chandler LM, Fahrenkrog AM, Kirst M, Gitzendanner MA, Soltis DE, Soltis PS. Linking genome signatures of selection and adaptation in non-model plants: exploring potential and limitations in the angiosperm Amborella. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:81-89. [PMID: 29694936 DOI: 10.1016/j.pbi.2018.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/24/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
Selective sweeps may be caused by environmental conditions that select for a gene function or trait at one locus, causing reduced variation at neighboring sites due to linkage, with specific non-selected variants being swept along with the selected variant. For many species, genomic and environmental data are available to test hypotheses that environmental conditions are correlated with selected regions. Most genomic studies relating selection to environment use model organisms or crop species; typically, these studies have genomic data from large numbers of individuals and extensive environmental data. Here, we review studies associating selective sweeps with environment and consider the impediments to successful application of these methods to non-model species. We present an initial investigation into linking genomic regions of selection to environmental conditions in the narrowly distributed, non-model plant Amborella trichopoda (Amborellaceae), the sister species to all other living flowering plants and one of over 2500 plant species endemic to New Caledonia.
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Affiliation(s)
- Richard Gj Hodel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Luke M Chandler
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Annette M Fahrenkrog
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | | | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; The Genetics Institute, University of Florida, Gainesville, FL 32610, USA; The Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA.
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124
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Seyfferth C, Wessels B, Jokipii-Lukkari S, Sundberg B, Delhomme N, Felten J, Tuominen H. Ethylene-Related Gene Expression Networks in Wood Formation. FRONTIERS IN PLANT SCIENCE 2018; 9:272. [PMID: 29593753 PMCID: PMC5861219 DOI: 10.3389/fpls.2018.00272] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 05/27/2023]
Abstract
Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula) stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2) homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and potential targets for EIN3D and ERF transcription factors in Populus stem tissues, which can help to understand the range of ethylene targeted biological processes during secondary growth.
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Affiliation(s)
- Carolin Seyfferth
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bernard Wessels
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Judith Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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125
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Tsai CJ, Harding SA, Cooke JEK. Branching out: a new era of investigating physiological processes in forest trees using genomic tools. TREE PHYSIOLOGY 2018; 38:303-310. [PMID: 29506180 DOI: 10.1093/treephys/tpy026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Scott A Harding
- Warnell School of Forestry and Natural Resources, Department of Genetics and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
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126
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Ma L, Li G. FAR1-RELATED SEQUENCE (FRS) and FRS-RELATED FACTOR (FRF) Family Proteins in Arabidopsis Growth and Development. FRONTIERS IN PLANT SCIENCE 2018; 9:692. [PMID: 29930561 PMCID: PMC6000157 DOI: 10.3389/fpls.2018.00692] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/07/2018] [Indexed: 05/18/2023]
Abstract
Transposable elements make important contributions to adaptation and evolution of their host genomes. The well-characterized transposase-derived transcription factor FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homologue FAR-RED IMPAIRED RESPONSE1 (FAR1) have crucial functions in plant growth and development. In addition, FHY3 and FAR1 are the founding members of the FRS (FAR1-RELATED SEQUENCE) and FRF (FRS-RELATED FACTOR) families, which are conserved among land plants. Although the coding sequences of many putative FRS and FRF orthologs have been found in various clades of angiosperms, their physiological functions remain elusive. Here, we summarize recent progress toward characterizing the molecular mechanisms of FHY3 and FAR1, as well as other FRS-FRF family proteins, examining their roles in regulating plant growth and development. This review also suggests future directions for further functional characterization of other FRS-FRF family proteins in plants.
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Affiliation(s)
- Lin Ma
- School of Biological Science and Technology, University of Jinan, Jinan, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Gang Li,
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127
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Oksanen E, Lihavainen J, Keinänen M, Keski-Saari S, Kontunen-Soppela S, Sellin A, Sõber A. Northern Forest Trees Under Increasing Atmospheric Humidity. PROGRESS IN BOTANY 2018:317-336. [PMID: 0 DOI: 10.1007/124_2017_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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128
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Matthews B, Best RJ, Feulner PGD, Narwani A, Limberger R. Evolution as an ecosystem process: insights from genomics. Genome 2017; 61:298-309. [PMID: 29241022 DOI: 10.1139/gen-2017-0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.
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Affiliation(s)
- Blake Matthews
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Rebecca J Best
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,b School of Earth Sciences and Environmental Sustainability, Northern Arizona University, 525 S. Beaver Street, Flagstaff, AZ 86011, USA
| | - Philine G D Feulner
- c Eawag, Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,d University of Bern, Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, Bern, Switzerland
| | - Anita Narwani
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Romana Limberger
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,e Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
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