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Li LL, Xiao Y, Wang X, He ZH, Lv YW, Hu XS. The Ka /Ks and πa /πs Ratios under Different Models of Gametophytic and Sporophytic Selection. Genome Biol Evol 2023; 15:evad151. [PMID: 37561000 PMCID: PMC10443736 DOI: 10.1093/gbe/evad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.
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Affiliation(s)
- Ling-Ling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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Abstract
Detection of secreted proteins and peptides during pollen tube guidance has been impeded due to lack of techniques to capture the pollen tube secretome without contamination from the female secreted proteins. Here we present a protocol to detect tobacco pollen tube secreted proteins, semi-in vivo pollen tube secretome assay (SIV-PS), following pollen tube crosstalk with the female reproductive tissues. This method combines the advantages of in vivo pollen tube-pistil interaction and filter-aided sample preparation (FASP) techniques to obtain an in-depth proteome coverage. The SIV-PS method is rapid, efficient, inexpensive, does not require specialized equipment or expertise, and provides a snapshot of the ongoing molecular interplay. We show that the secretome obtained is of greater purity (<1.4% ADH activities) and that pollen tubes are physiologically and cytologically unaffected. A compendium of quality controls is described and a rough guide on downstream bioinformatics analysis is outlined. The SIV-PS method is applicable to all studies of protein secretion using pollen tube as a model and can be easily adapted to other flowering species with modification. The overall duration for this protocol is approximately 8 hours spanning 4 days (an average of 2 h/day per two workers) excluding microscopy and LC-MS/MS analysis.
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Kulichová K, Kumar V, Steinbachová L, Klodová B, Timofejeva L, Juříček M, Honys D, Hafidh S. PRP8A and PRP8B spliceosome subunits act co-ordinately to control pollen tube attraction in Arabidopsis. Development 2020; 147:dev.186742. [DOI: 10.1242/dev.186742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023]
Abstract
Precise guided pollen tube growth by the female gametophyte is a pre-requisite for successful sexual reproduction in flowering plants. Cysteine-rich proteins (CRPs) secreted from the embryo sac are known pollen tube attractants perceived by pollen tube receptor-like kinases (RLK's). How pre-mRNA splicing facilitates this cell-to-cell communication is not understood. Here, we report novel function of Pre-mRNA PROCESSING factor 8 paralogs, PRP8A and PRP8B, as regulators of pollen tube attraction. Double mutant prp8a prp8b ovules cannot attract pollen tubes, and prp8a prp8b pollen tubes fail in sensing ovules attraction signals. Only 3% of ovule-expressed genes were misregulated in prp8a prp8b. Combination of RNA-seq and MYB98/LURE1.2-YFP reporter revealed the expression of MYB98, LUREs and 49 other CRPs were downregulated suggesting loss of synergid cell fate. Differential Exon usage (DEU) and Intron-retention (IR) analysis revealed autoregulation of PPR8A/PRP8B splicing. In vivo, PRP8A coimmunoprecipitates with splicing enhancer AtSF3A1, suggesting involvement of PRP8A in 3′-splice site selection. Our data hint that PRP8A/PRP8B module exhibit spliceosome-autoregulation to facilitate pollen tube attraction via transcriptional regulation of MYB98, CRPs and LURE pollen tube attractants.
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Affiliation(s)
- Katarína Kulichová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Božena Klodová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Ljudmilla Timofejeva
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Miloslav Juříček
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
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Joly V, Tebbji F, Nantel A, Matton DP. Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis. PLANTS (BASEL, SWITZERLAND) 2019; 8:E185. [PMID: 31238522 PMCID: PMC6630372 DOI: 10.3390/plants8060185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]
Abstract
Sexual reproduction in flowering plants involves intimate contact and continuous interactions between the growing pollen tube and the female reproductive structures. These interactions can trigger responses in distal regions of the flower well ahead of fertilization. While pollination-induced petal senescence has been studied extensively, less is known about how pollination is perceived at a distance in the ovary, and how specific this response is to various pollen genotypes. To address this question, we performed a global transcriptomic analysis in the ovary of a wild potato species, Solanum chacoense, at various time points following compatible, incompatible, and heterospecific pollinations. In all cases, pollen tube penetration in the stigma was initially perceived as a wounding aggression. Then, as the pollen tubes grew in the style, a growing number of genes became specific to each pollen genotype. Functional classification analyses revealed sharp differences in the response to compatible and heterospecific pollinations. For instance, the former induced reactive oxygen species (ROS)-related genes while the latter affected genes associated to ethylene signaling. In contrast, incompatible pollination remained more akin to a wound response. Our analysis reveals that every pollination type produces a specific molecular signature generating diversified and specific responses at a distance in the ovary in preparation for fertilization.
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Affiliation(s)
- Valentin Joly
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC H1X 2B2, Canada.
| | - Faïza Tebbji
- CRCHU de Québec, Université Laval, Québec, QC G1V 4G2, Canada.
| | - André Nantel
- National Research Council Canada, Montréal, QC H4P 2R2, Canada.
| | - Daniel P Matton
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC H1X 2B2, Canada.
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Zheng YY, Lin XJ, Liang HM, Wang FF, Chen LY. The Long Journey of Pollen Tube in the Pistil. Int J Mol Sci 2018; 19:E3529. [PMID: 30423936 PMCID: PMC6275014 DOI: 10.3390/ijms19113529] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022] Open
Abstract
In non-cleistogamous plants, the male gametophyte, the pollen grain is immotile and exploits various agents, such as pollinators, wind, and even water, to arrive to a receptive stigma. The complex process of pollination involves a tubular structure, i.e., the pollen tube, which delivers the two sperm cells to the female gametophyte to enable double fertilization. The pollen tube has to penetrate the stigma, grow in the style tissues, pass through the septum, grow along the funiculus, and navigate to the micropyle of the ovule. It is a long journey for the pollen tube and its two sperm cells before they meet the female gametophyte, and it requires very accurate regulation to perform successful fertilization. In this review, we update the knowledge of molecular dialogues of pollen-pistil interaction, especially the progress of pollen tube activation and guidance, and give perspectives for future research.
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Affiliation(s)
- Yang-Yang Zheng
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xian-Ju Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hui-Min Liang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Fang-Fei Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Li-Yu Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center for Genomics and Biotechnology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Tremblay RR, Bourassa S, Nehmé B, Calvo EL. Daylily protein constituents of the pollen and stigma a proteomics approach. JOURNAL OF PLANT PHYSIOLOGY 2017; 212:1-12. [PMID: 28242413 DOI: 10.1016/j.jplph.2017.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
This study was aimed at the identification and quantification of the protein components of the pollen grains in parallel with the distal stigmatic tissue of tetraploid cultivars. Proteomes were analyzed using iTRAQ 4plex labeling, peptides separation by online RP-nano-LC and analysis by ESI-MS/MS. Protein identification and quantification were made using the Asparagales database as a reference. A total of 524,037 MS/MS spectra were produced from pollen and stigma samples. From these, a total of 8368 peptides wereidentified corresponding to 994 unique peptides and 432 protein groups. Among them, 128 differentially expressed proteins were retained for further analysis. In absence of the daylily genome availability, we exploited numerous databases and bioinformatics resources to exploring the putative biological functions of these proteins. The profile of differentially expressed proteins suggests an important representation of functions associated to the signalling and response against endogenous and environmental stresses, including several enzymes implicated in the biosynthesis of antibiotics. The abundance in stigma of several structural proteins of the ribosomal sub-units as well as of the core histones suggest that the translation processes and the regulation of gene expression in stigma is a more active mechanism than in pollen. In addition, pollen prioritizes the synthesis of fructose and glucose as opposed to sucrose in stigma as a source of energy. Finally, the modulated proteins in Hemerocallis point to several pathways that give potential clues concerning the molecular mechanisms underlying the functions of the pollen and the stigmatic fluid in daylily reproduction.
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Affiliation(s)
- Roland R Tremblay
- CHUL Research Center in Reproduction, Centre de Recherche du CHU de Québec,2705 Boulevard Laurier, Suite T3-67, Quebec City, QC, G1 V 4G2, Canada.
| | - Sylvie Bourassa
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Benjamin Nehmé
- Proteomics Platform Quebec Genomics Center, CRCHUL, Centre de Recherche du CHU de Quebec, Canada.
| | - Ezequiel L Calvo
- Scientific Consultant in Genomics, 701 Leonard, Quebec City, QC, G1X 4C9, Canada.
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Losada JM, Herrero M. Pollen tube access to the ovule is mediated by glycoprotein secretion on the obturator of apple (Malus × domestica, Borkh). ANNALS OF BOTANY 2017; 119:989-1000. [PMID: 28137704 PMCID: PMC5604596 DOI: 10.1093/aob/mcw276] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 05/31/2023]
Abstract
BACKGROUND AND AIMS Within the ovary, the obturator bridges the pathway of the pollen tube from the style to the ovule. Despite its widespread presence among flowering plants, its function has only been studied in a handful of species, and the molecules involved in pollen tube-obturator cross-talk have not been explored hitherto. This work evaluates the involvement of glucans and glycoproteins on pollen tube growth in the obturator of apple flowers ( Malus × domestica) . METHODS Pollen tube kinetics were sequentially examined in the pistil and related to changes occurring on the obturator using histochemistry and inmunocytochemistry. To discriminate between changes in the obturator induced by pollen tubes from those developmentally regulated, both pollinated and unpollinated pistils were examined. KEY RESULTS Pollen tube growth rates were slow in the stigma, faster in the style and slow again in the ovary. The arrival of pollen tubes at the obturator was concomitant with the secretion of proteins, saccharides and glycoprotein epitopes belonging to extensins and arabinogalactan proteins (AGPs). While some of these secretions - extensins and AGPs labelled by JIM13 - were developmentally regulated, others - AGPs labelled by JIM8 - were elicited by the presence of pollen tubes. Following pollen tube passage, all these glycoproteins were depleted. CONCLUSIONS The results show a timely secretion of glycoproteins on the obturator surface concomitant with pollen tube arrival at this structure. The fact that their secretion is depleted following pollen tube passage strongly suggests their role in regulating pollen tube access to the ovule. Remarkably, both the regulation of the secretion of the different glycoproteins, as well as their association with the performance of pollen tubes exhibit similarities with those observed in the stigma, in line with their common developmental origin.
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Affiliation(s)
- Juan M. Losada
- Arnold Arboretum of Harvard University, 1300 Centre St, Boston, MA 02131, USA
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, MA 02138, USA
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, RI 02912, USA
- Pomology Department, Aula Dei Experimental Station-CSIC, Avda Montañana 1005, 50059 Zaragoza, Spain
| | - Maria Herrero
- Pomology Department, Aula Dei Experimental Station-CSIC, Avda Montañana 1005, 50059 Zaragoza, Spain
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Abstract
New insights into the molecular dialogue between male and female during sexual plant reproduction show that even plant sex does not work without clear communication. Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0928-x
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