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Cheng M, Yuan H, Wang R, Zou J, Liang T, Yang F, Li S. Genome-Wide Identification and Analysis of the Metallothionein Genes in Oryza Genus. Int J Mol Sci 2021; 22:ijms22179651. [PMID: 34502554 PMCID: PMC8431808 DOI: 10.3390/ijms22179651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 11/22/2022] Open
Abstract
Metallothionein (MT) proteins are low molecular mass, cysteine-rich, and metal-binding proteins that play an important role in maintaining metal homeostasis and stress response. However, the evolutionary relationships and functional differentiation of MT in the Oryza genus remain unclear. Here we identified 53 MT genes from six Oryza genera, including O. sativa ssp. japonica, O. rufipogon, O. sativa ssp. indica, O. nivara, O. glumaepatula, and O. barthii. The MT genes were clustered into four groups based on phylogenetic analysis. MT genes are unevenly distributed on chromosomes; almost half of the MT genes were clustered on chromosome 12, which may result from a fragment duplication containing the MT genes on chromosome 12. Five pairs of segmental duplication events and ten pairs of tandem duplication events were found in the rice MT family. The Ka/Ks values of the fifteen duplicated MT genes indicated that the duplicated MT genes were under a strong negative selection during evolution. Next, combining the promoter activity assay with gene expression analysis revealed different expression patterns of MT genes. In addition, the expression of OsMT genes was induced under different stresses, including NaCl, CdCl2, ABA, and MeJ treatments. Additionally, we found that OsMT genes were mainly located in chloroplasts. These results imply that OsMT genes play different roles in response to these stresses. All results provide important insights into the evolution of the MT gene family in the Oryza genus, and will be helpful to further study the function of MT genes.
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Hassani‐Pak K, Singh A, Brandizi M, Hearnshaw J, Parsons JD, Amberkar S, Phillips AL, Doonan JH, Rawlings C. KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1670-1678. [PMID: 33750020 PMCID: PMC8384599 DOI: 10.1111/pbi.13583] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
The generation of new ideas and scientific hypotheses is often the result of extensive literature and database searches, but, with the growing wealth of public and private knowledge, the process of searching diverse and interconnected data to generate new insights into genes, gene networks, traits and diseases is becoming both more complex and more time-consuming. To guide this technically challenging data integration task and to make gene discovery and hypotheses generation easier for researchers, we have developed a comprehensive software package called KnetMiner which is open-source and containerized for easy use. KnetMiner is an integrated, intelligent, interactive gene and gene network discovery platform that supports scientists explore and understand the biological stories of complex traits and diseases across species. It features fast algorithms for generating rich interactive gene networks and prioritizing candidate genes based on knowledge mining approaches. KnetMiner is used in many plant science institutions and has been adopted by several plant breeding organizations to accelerate gene discovery. The software is generic and customizable and can therefore be readily applied to new species and data types; for example, it has been applied to pest insects and fungal pathogens; and most recently repurposed to support COVID-19 research. Here, we give an overview of the main approaches behind KnetMiner and we report plant-centric case studies for identifying genes, gene networks and trait relationships in Triticum aestivum (bread wheat), as well as, an evidence-based approach to rank candidate genes under a large Arabidopsis thaliana QTL. KnetMiner is available at: https://knetminer.org.
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Orozco-Arias S, Candamil-Cortés MS, Jaimes PA, Piña JS, Tabares-Soto R, Guyot R, Isaza G. K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes. PeerJ 2021; 9:e11456. [PMID: 34055489 PMCID: PMC8140598 DOI: 10.7717/peerj.11456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/24/2021] [Indexed: 12/15/2022] Open
Abstract
Every day more plant genomes are available in public databases and additional massive sequencing projects (i.e., that aim to sequence thousands of individuals) are formulated and released. Nevertheless, there are not enough automatic tools to analyze this large amount of genomic information. LTR retrotransposons are the most frequent repetitive sequences in plant genomes; however, their detection and classification are commonly performed using semi-automatic and time-consuming programs. Despite the availability of several bioinformatic tools that follow different approaches to detect and classify them, none of these tools can individually obtain accurate results. Here, we used Machine Learning algorithms based on k-mer counts to classify LTR retrotransposons from other genomic sequences and into lineages/families with an F1-Score of 95%, contributing to develop a free-alignment and automatic method to analyze these sequences.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.,Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia
| | | | - Paula A Jaimes
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | - Johan S Piña
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | - Reinel Tabares-Soto
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia
| | - Romain Guyot
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Caldas, Colombia.,Institut de Recherche pour le Développement, CIRAD, Univ. Montpellier, Montpellier, France
| | - Gustavo Isaza
- Department of Systems and Informatics, Universidad de Caldas, Manizales, Caldas, Colombia
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Xu X, Zhang L, Zhao W, Fu L, Han Y, Wang K, Yan L, Li Y, Zhang XH, Min DH. Genome-wide analysis of the serine carboxypeptidase-like protein family in Triticum aestivum reveals TaSCPL184-6D is involved in abiotic stress response. BMC Genomics 2021; 22:350. [PMID: 33992092 PMCID: PMC8126144 DOI: 10.1186/s12864-021-07647-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/21/2021] [Indexed: 12/17/2022] Open
Abstract
Background The serine carboxypeptidase-like protein (SCPL) family plays a vital role in stress response, growth, development and pathogen defense. However, the identification and functional analysis of SCPL gene family members have not yet been performed in wheat. Results In this study, we identified a total of 210 candidate genes encoding SCPL proteins in wheat. According to their structural characteristics, it is possible to divide these members into three subfamilies: CPI, CPII and CPIII. We uncovered a total of 209 TaSCPL genes unevenly distributed across 21 wheat chromosomes, of which 65.7% are present in triads. Gene duplication analysis showed that ~ 10.5% and ~ 64.8% of the TaSCPL genes are derived from tandem and segmental duplication events, respectively. Moreover, the Ka/Ks ratios between duplicated TaSCPL gene pairs were lower than 0.6, which suggests the action of strong purifying selection. Gene structure analysis showed that most of the TaSCPL genes contain multiple introns and that the motifs present in each subfamily are relatively conserved. Our analysis on cis-acting elements showed that the promoter sequences of TaSCPL genes are enriched in drought-, ABA- and MeJA-responsive elements. In addition, we studied the expression profiles of TaSCPL genes in different tissues at different developmental stages. We then evaluated the expression levels of four TaSCPL genes by qRT-PCR, and selected TaSCPL184-6D for further downstream analysis. The results showed an enhanced drought and salt tolerance among TaSCPL184-6D transgenic Arabidopsis plants, and that the overexpression of the gene increased proline and decreased malondialdehyde levels, which might help plants adapting to adverse environments. Our results provide comprehensive analyses of wheat SCPL genes that might work as a reference for future studies aimed at improving drought and salt tolerance in wheat. Conclusions We conducte a comprehensive bioinformatic analysis of the TaSCPL gene family in wheat, which revealing the potential roles of TaSCPL genes in abiotic stress. Our analysis also provides useful resources for improving the resistance of wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07647-6.
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Affiliation(s)
- Xiaomin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Wan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Liang Fu
- Xinxiang Academy of Agricultural Sciences of He'nan Province, Xinxiang, China
| | - Yuxuan Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Keke Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Luyu Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiao-Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Dong-Hong Min
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
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Heidari P, Faraji S, Ahmadizadeh M, Ahmar S, Mora-Poblete F. New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis. Front Genet 2021; 12:657970. [PMID: 34054921 PMCID: PMC8155530 DOI: 10.3389/fgene.2021.657970] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 12/19/2022] Open
Abstract
The TIFY gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of TIFY genes in plant species can reveal more details. In the current study, the members of the TIFY gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the TIFY gene family between 48 tomato (Solanum lycopersicum, a dicot plant) genes and 26 maize (Zea mays, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, TIFY family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the TIFY gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of TIFY genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato TIFY genes showed that TIFY genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.
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Affiliation(s)
- Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, Shahrood, Iran
| | - Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | | | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, Talca, Chile
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Li M, Xiao Y, Mount S, Liu Z. An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals. FRONTIERS IN PLANT SCIENCE 2021; 12:644881. [PMID: 33868343 PMCID: PMC8047320 DOI: 10.3389/fpls.2021.644881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/22/2021] [Indexed: 05/12/2023]
Abstract
Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.
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Affiliation(s)
| | | | | | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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57
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Faraji S, Ahmadizadeh M, Heidari P. Genome-wide comparative analysis of Mg transporter gene family between Triticum turgidum and Camelina sativa. Biometals 2021; 34:639-660. [PMID: 33783656 DOI: 10.1007/s10534-021-00301-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/16/2021] [Indexed: 12/21/2022]
Abstract
Magnesium (Mg) as a bimetal plays critical roles in biochemical processes, membrane stability, and enzyme activity. Mg transporters (MGTs) are involving in maintaining Mg homeostasis in cells. Although the MGT family members have been identified in different plant species, there is no comprehensive analysis of the other plants' MGT genes. In the current study, 62 and 41 non-redundant putative MGT proteins were recognized into the genome of Camelina sativa, and Triticum turgidum and they were compared based on physicochemical properties, protein structure, expression, and interaction. All identified MGTs were classified into three subgroups, NIPA, CorA, and MRS2/MGT, based on conserved-motifs distribution. The results showed that the secondary structure pattern in NIPA and MRS2 subfamily members in both studied plant species were highly similar. Furthermore, MGTs encompass the conserved structures and the critical sites mainly in the metal ion and Mg2+ binding centers as well as the catalytic sites were observed. The highest numbers of protein channels were predicted in CorA proteins in both C. sativa and T. turgidum with 24 and 17 channel numbers, respectively. The Ser, Pro, Gly, Lys, Tyr, and Arg amino acids were predicted as the binding residues in MGTs channel regions. The expression pattern of identified genes demonstrated that MGT genes have diverse tissue-specific expression and stress response expression patterns. Besides, 147 co-expressed genes with MGTs were clustered into the eight co-expression nodes involved in N-glycan biosynthesis, protein processing in the endoplasmic reticulum, carbon metabolism, biosynthesis of amino acids, and endocytosis. In the present study, all interpretations are based on in silico predictions, which can be used in further studies related to functional genomics of MGT genes.
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Affiliation(s)
- Sahar Faraji
- Department of Plant Breeding, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University (SANRU), 4818168984, Sari, Iran
| | | | - Parviz Heidari
- Faculty of Agriculture, Shahrood University of Technology, 3619995161, Shahrood, Iran.
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58
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Errum A, Rehman N, Khan MR, Ali GM. Genome-wide characterization and expression analysis of pseudo-response regulator gene family in wheat. Mol Biol Rep 2021; 48:2411-2427. [PMID: 33782785 DOI: 10.1007/s11033-021-06276-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/11/2021] [Indexed: 11/29/2022]
Abstract
Pseudo-response regulator (PRR) gene family members play a significant role in plant circadian clocks, flowering time inflorescence architecture development during transition from vegetative growth phase to reproductive phase. In current study, we analyzed the expression profiling, phylogenetic relationship, and molecular characterization of PRR gene family members of common wheat by using IWGSC Ref seq v1.1 wheat genome database with a coverage rate of 90%. By using bioinformatic approach total 20 candidate gene sequences were identified and divided into six groups and four clades. It was found that mostly genes have same number of exons and introns showed similar features because they originated through duplication events during evolution processes. Although all the proteins have conserved PRR domains, but some are distinct in their sequences suggesting functional divergence. By comparative synteny analysis it was revealed that Group 1, 2, 3 and 11-D of group 4 have duplication events while group 5 and TaPRR9-B,10-D showed conservation with previously identified PRR members from rice. While expression variation of six groups from each analysis matches with each other. Five groups highly expressed in leaf, spike, and roots in pattern like leaf > spike > root at all three stages booting, heading and anthesis of spike development. This suggests that TaPRR genes play important roles in different photoperiod signaling pathways in different organs at different stages of spike development and flowering via unknown pathway. These findings will also provide comprehensive knowledge about future investigations on wheat PRR family members involved in complex network of circadian system for plant development.
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Affiliation(s)
- Aliya Errum
- Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Muhammad Ramzan Khan
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Ghulam Muhammad Ali
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan.,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
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59
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Pei T, Yan M, Kong Y, Fan H, Liu J, Cui M, Fang Y, Ge B, Yang J, Zhao Q. The genome of Tripterygium wilfordii and characterization of the celastrol biosynthesis pathway. GIGABYTE 2021; 2021:gigabyte14. [PMID: 36967728 PMCID: PMC10038137 DOI: 10.46471/gigabyte.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/25/2021] [Indexed: 11/09/2022] Open
Abstract
Tripterygium wilfordii is a vine from the Celastraceae family that is used in traditional Chinese medicine (TCM). The active ingredient, celastrol, is a friedelane-type pentacyclic triterpenoid with putative roles as an antitumor, immunosuppressive, and anti-obesity agent. Here, we report a reference genome assembly of T. wilfordii with high-quality annotation using a hybrid sequencing strategy. The total genome size obtained is 340.12 Mb, with a contig N50 value of 3.09 Mb. We successfully anchored 91.02% of sequences into 23 pseudochromosomes using high-throughput chromosome conformation capture (Hi–C) technology. The super-scaffold N50 value was 13.03 Mb. We also annotated 31,593 structural genes, with a repeat percentage of 44.31%. These data demonstrate that T. wilfordii diverged from Malpighiales species approximately 102.4 million years ago. By integrating genome, transcriptome and metabolite analyses, as well as in vivo and in vitro enzyme assays of two cytochrome P450 (CYP450) genes, TwCYP712K1 and TwCYP712K2, it is possible to investigate the second biosynthesis step of celastrol and demonstrate that this was derived from a common ancestor. These data provide insights and resources for further investigation of pathways related to celastrol, and valuable information to aid the conservation of resources, as well as understand the evolution of Celastrales.
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Affiliation(s)
- Tianlin Pei
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Hang Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Mengying Cui
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yumin Fang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Binjie Ge
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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60
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Pieper R, Tomé F, Pankin A, von Korff M. FLOWERING LOCUS T4 delays flowering and decreases floret fertility in barley. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:107-121. [PMID: 33048122 PMCID: PMC7816854 DOI: 10.1093/jxb/eraa466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/07/2020] [Indexed: 05/04/2023]
Abstract
FLOWERING LOCUS T-like (FT-like) genes control the photoperiodic regulation of flowering in many angiosperm plants. The family of FT-like genes is characterized by extensive gene duplication and subsequent diversification of FT functions which occurred independently in modern angiosperm lineages. In barley, there are 12 known FT-like genes (HvFT), but the function of most of them remains uncharacterized. This study aimed to characterize the role of HvFT4 in flowering time control and development in barley. The overexpression of HvFT4 in the spring cultivar Golden Promise delayed flowering time under long-day conditions. Microscopic dissection of the shoot apical meristem revealed that overexpression of HvFT4 specifically delayed spikelet initiation and reduced the number of spikelet primordia and grains per spike. Furthermore, ectopic overexpression of HvFT4 was associated with floret abortion and with the down-regulation of the barley MADS-box genes VRN-H1, HvBM3, and HvBM8 which promote floral development. This suggests that HvFT4 functions as a repressor of reproductive development in barley. Unraveling the genetic basis of FT-like genes can contribute to the identification of novel breeding targets to modify reproductive development and thereby spike morphology and grain yield.
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Affiliation(s)
- Rebecca Pieper
- Institute for Plant Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Filipa Tomé
- Institute for Plant Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, ‘SMART Plants for Tomorrow’s Needs’, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Artem Pankin
- Institute for Plant Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, ‘SMART Plants for Tomorrow’s Needs’, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, ‘SMART Plants for Tomorrow’s Needs’, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Correspondence:
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61
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The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses. Genes (Basel) 2020; 11:genes11121464. [PMID: 33297327 PMCID: PMC7762271 DOI: 10.3390/genes11121464] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat.
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Chen Y, Song W, Xie X, Wang Z, Guan P, Peng H, Jiao Y, Ni Z, Sun Q, Guo W. A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. MOLECULAR PLANT 2020; 13:1694-1708. [PMID: 32979565 DOI: 10.1016/j.molp.2020.09.019] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/03/2020] [Accepted: 09/21/2020] [Indexed: 05/18/2023]
Abstract
Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.
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Affiliation(s)
- Yongming Chen
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Wanjun Song
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Beijing Geek Gene Technology Co Ltd, Beijing 100193, China
| | - Xiaoming Xie
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Panfeng Guan
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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63
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Grosjean N, Blaby-Haas CE. Leveraging computational genomics to understand the molecular basis of metal homeostasis. THE NEW PHYTOLOGIST 2020; 228:1472-1489. [PMID: 32696981 DOI: 10.1111/nph.16820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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64
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Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E. PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PLANT DIRECT 2020; 4:e00293. [PMID: 33392435 PMCID: PMC7773024 DOI: 10.1002/pld3.293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 05/22/2023]
Abstract
We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to duplications of individual genes and whole genomes in plant lineages. Such duplications result in complex evolutionary relationships between related genes, which may have similar sequences but highly divergent functions. In such cases, functional inference requires more than a simple sequence similarity calculation. We have developed an online resource, PhyloGenes (phylogenes.org), that displays precomputed phylogenetic trees for plant gene families along with experimentally validated function information for individual genes within the families. A total of 40 plant genomes and 10 non-plant model organisms are represented in over 8,000 gene families. Evolutionary events such as speciation and duplication are clearly labeled on gene trees to distinguish orthologs from paralogs. Nearly 6,000 families have at least one member with an experimentally supported annotation to a Gene Ontology (GO) molecular function or biological process term. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes facilitates the use of evolutionary history to determine the most likely function of genes that have not been experimentally characterized. Future work will enrich the resource by incorporating additional gene function datasets such as plant gene expression atlas data.
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Affiliation(s)
| | | | - Dustin Ebert
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Qian Li
- Phoenix BioinformaticsFremontCAUSA
| | - Huaiyu Mi
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Anushya Muruganujan
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | | | | | - Paul D. Thomas
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
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65
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Ge SX, Jung D, Yao R. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics 2020; 36:2628-2629. [PMID: 31882993 DOI: 10.1093/bioinformatics/btz931] [Citation(s) in RCA: 1629] [Impact Index Per Article: 407.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/04/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as gene ontology (GO) and other databases. RESULTS To complement existing tools, we developed ShinyGO based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archeal and 1678 bacterial species. ShinyGO's novel features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for the retrieval of pathway diagrams and protein-protein interaction networks. ShinyGO is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets. AVAILABILITY AND IMPLEMENTATION http://ge-lab.org/go/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, Brookings, SD 57007, USA
| | - Dongmin Jung
- Department of Mathematics and Statistics, Brookings, SD 57007, USA.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Runan Yao
- Department of Mathematics and Statistics, Brookings, SD 57007, USA
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66
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Hao L, Shi S, Guo H, Li M, Hu P, Wei Y, Feng Y. Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays. PeerJ 2020; 8:e9551. [PMID: 32742811 PMCID: PMC7370932 DOI: 10.7717/peerj.9551] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.
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Affiliation(s)
- Lidong Hao
- College of Agriculture, Xinjiang Agriculture University, Urumqi, China.,College of Agriculture and Hydraulic Engineering, Sui Hua University, Suihua, China
| | - Shubing Shi
- College of Agriculture, Xinjiang Agriculture University, Urumqi, China
| | - Haibin Guo
- College of Agriculture and Hydraulic Engineering, Sui Hua University, Suihua, China
| | - Ming Li
- School of Economics and Management, Sui Hua University, Suihua, China
| | - Pan Hu
- College of Agriculture and Hydraulic Engineering, Sui Hua University, Suihua, China
| | - Yadong Wei
- College of Agriculture, Xinjiang Agriculture University, Urumqi, China
| | - Yanfei Feng
- College of Agriculture and Hydraulic Engineering, Sui Hua University, Suihua, China
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Yang X, Guo X, Chen G, Dong D, Liu F, Yang Y, Yang Y, Li G. Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling. PeerJ 2020; 8:e9096. [PMID: 32411536 PMCID: PMC7207217 DOI: 10.7717/peerj.9096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao Guo
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Daofeng Dong
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Fang Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yu Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing, China
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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69
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Li Q, Qin Y, Hu X, Li G, Ding H, Xiong X, Wang W. Transcriptome analysis uncovers the gene expression profile of salt-stressed potato (Solanum tuberosum L.). Sci Rep 2020; 10:5411. [PMID: 32214109 PMCID: PMC7096413 DOI: 10.1038/s41598-020-62057-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/05/2020] [Indexed: 12/14/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important staple food worldwide. However, its growth has been heavily suppressed by salt stress. The molecular mechanisms of salt tolerance in potato remain unclear. It has been shown that the tetraploid potato Longshu No. 5 is a salt-tolerant genotype. Therefore, in this study we conducted research to identify salt stress response genes in Longshu No. 5 using a NaCl treatment and time-course RNA sequencing. The total number of differentially expressed genes (DEGs) in response to salt stress was 5508. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it was found that DEGs were significantly enriched in the categories of nucleic acid binding, transporter activity, ion or molecule transport, ion binding, kinase activity and oxidative phosphorylation. Particularly, the significant differential expression of encoding ion transport signaling genes suggests that this signaling pathway plays a vital role in salt stress response in potato. Finally, the DEGs in the salt response pathway were verified by Quantitative real-time PCR (qRT-PCR). These results provide valuable information on the salt tolerance of molecular mechanisms in potatoes, and establish a basis for breeding salt-tolerant cultivars.
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Affiliation(s)
- Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Yuzhi Qin
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Xinxi Hu
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Hongying Ding
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China
| | - Xingyao Xiong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
- College of Horticulture, Hunan Agricultural University/Hunan Provincial Engineering Research Center for Potatoes/Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, 410128, China.
| | - Wanxing Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Root and Tuber Crops, Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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70
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Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans. G3-GENES GENOMES GENETICS 2020; 10:623-634. [PMID: 31818876 PMCID: PMC7003068 DOI: 10.1534/g3.119.400818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.
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Yang X, Yang Y, Ling J, Guan J, Guo X, Dong D, Jin L, Huang S, Liu J, Li G. A high-throughput BAC end analysis protocol (BAC-anchor) for profiling genome assembly and physical mapping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:364-372. [PMID: 31254434 PMCID: PMC6953197 DOI: 10.1111/pbi.13203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Traditional approaches for sequencing insertion ends of bacterial artificial chromosome (BAC) libraries are laborious and expensive, which are currently some of the bottlenecks limiting a better understanding of the genomic features of auto- or allopolyploid species. Here, we developed a highly efficient and low-cost BAC end analysis protocol, named BAC-anchor, to identify paired-end reads containing large internal gaps. Our approach mainly focused on the identification of high-throughput sequencing reads carrying restriction enzyme cutting sites and searching for large internal gaps based on the mapping locations of both ends of the reads. We sequenced and analysed eight libraries containing over 3 200 000 BAC end clones derived from the BAC library of the tetraploid potato cultivar C88 digested with two restriction enzymes, Cla I and Mlu I. About 25% of the BAC end reads carrying cutting sites generated a 60-100 kb internal gap in the potato DM reference genome, which was consistent with the mapping results of Sanger sequencing of the BAC end clones and indicated large differences between autotetraploid and haploid genotypes in potato. A total of 5341 Cla I- and 165 Mlu I-derived unique reads were distributed on different chromosomes of the DM reference genome and could be used to establish a physical map of target regions and assemble the C88 genome. The reads that matched different chromosomes are especially significant for the further assembly of complex polyploid genomes. Our study provides an example of analysing high-coverage BAC end libraries with low sequencing cost and is a resource for further genome sequencing studies.
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Affiliation(s)
- Xiaohui Yang
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural SciencesMolecular Biology Key Laboratory of Shandong Facility VegetableNational Vegetable Improvement Center Shandong Sub‐CenterHuang‐Huai‐Hai Region Scientific Observation and Experimental Station of VegetablesMinistry of Agriculture and Rural AffairsJinanChina
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijingChina
| | - Yu Yang
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural SciencesMolecular Biology Key Laboratory of Shandong Facility VegetableNational Vegetable Improvement Center Shandong Sub‐CenterHuang‐Huai‐Hai Region Scientific Observation and Experimental Station of VegetablesMinistry of Agriculture and Rural AffairsJinanChina
| | - Jian Ling
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijingChina
| | - Jiantao Guan
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Resources and Genetic ImprovementBeijingChina
| | - Xiao Guo
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural SciencesMolecular Biology Key Laboratory of Shandong Facility VegetableNational Vegetable Improvement Center Shandong Sub‐CenterHuang‐Huai‐Hai Region Scientific Observation and Experimental Station of VegetablesMinistry of Agriculture and Rural AffairsJinanChina
| | - Daofeng Dong
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural SciencesMolecular Biology Key Laboratory of Shandong Facility VegetableNational Vegetable Improvement Center Shandong Sub‐CenterHuang‐Huai‐Hai Region Scientific Observation and Experimental Station of VegetablesMinistry of Agriculture and Rural AffairsJinanChina
| | - Liping Jin
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijingChina
| | - Sanwen Huang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijingChina
| | - Jun Liu
- Institute of Crop ScienceChinese Academy of Agricultural SciencesNational Key Facility for Crop Resources and Genetic ImprovementBeijingChina
| | - Guangcun Li
- Vegetable and Flower Research Institute of Shandong Academy of Agricultural SciencesMolecular Biology Key Laboratory of Shandong Facility VegetableNational Vegetable Improvement Center Shandong Sub‐CenterHuang‐Huai‐Hai Region Scientific Observation and Experimental Station of VegetablesMinistry of Agriculture and Rural AffairsJinanChina
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijingChina
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Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5513438. [PMID: 31210272 DOI: 10.1093/database/baz065] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 11/13/2022]
Abstract
GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.
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Affiliation(s)
- Victoria C Blake
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Margaret R Woodhouse
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Gerard R Lazo
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Sarah G Odell
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Yi Wang
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Yong Q Gu
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Clay L Birkett
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Jean-Luc Jannink
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Dave E Matthews
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - David L Hane
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Steve L Michel
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Eric Yao
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Taner Z Sen
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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73
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Zhou B, Yang Y, Zhan J, Dou X, Wang J, Zhou Y. Predicting functional long non-coding RNAs validated by low throughput experiments. RNA Biol 2019; 16:1555-1564. [PMID: 31345106 PMCID: PMC6779387 DOI: 10.1080/15476286.2019.1644590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/17/2019] [Accepted: 07/10/2019] [Indexed: 01/05/2023] Open
Abstract
High-throughput techniques have uncovered hundreds and thousands of long non-coding RNAs (lncRNAs). Among them, only a tiny fraction has experimentally validated functions (EVlncRNAs) by low-throughput methods. What fraction of lncRNAs from high-throughput experiments (HTlncRNAs) is truly functional is an active subject of debate. Here, we developed the first method to distinguish EVlncRNAs from HTlncRNAs and mRNAs by using Support Vector Machines and found that EVlncRNAs can be well separated from HTlncRNAs and mRNAs with 0.6 for Matthews correlation coefficient, 64% for sensitivity, and 81% for precision for the independent human test set. The most useful features for classification are related to sequence conservations at RNA (for separating from HTlncRNAs) and protein (for separating from mRNA) levels. The method is found to be robust as the human-RNA-trained model is applicable to independent mouse RNAs with similar accuracy and to a lesser extent to plant RNAs. The method can recover newly discovered EVlncRNAs with high sensitivity. Its application to randomly selected 2000 human HTlncRNAs indicates that the majority of HTlncRNAs is probably non-functional but a large portion (nearly 30%) are likely functional. In other words, there is an ample number of lncRNAs whose specific biological roles are yet to be discovered. The method developed here is expected to speed up and reduce the cost of the discovery by prioritizing potentially functional lncRNAs prior to experimental validation. EVlncRNA-pred is available as a web server at http://biophy.dzu.edu.cn/lncrnapred/index.html . All datasets used in this study can be obtained from the same website.
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Affiliation(s)
- Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- College of Physics and Electronic Information, Dezhou University, Dezhou, China
| | - Yuedong Yang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Xianghua Dou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- College of Physics and Electronic Information, Dezhou University, Dezhou, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- College of Physics and Electronic Information, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
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74
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Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, Coppens F, Vandepoele K. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res 2019; 46:D1190-D1196. [PMID: 29069403 PMCID: PMC5753339 DOI: 10.1093/nar/gkx1002] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/12/2017] [Indexed: 11/14/2022] Open
Abstract
PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.
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Affiliation(s)
- Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Tim Diels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Emmelien Vancaester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | | | | | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
- To whom correspondence should be addressed. Tel: +32 9 331 3822; Fax: +32 9 331 3809;
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75
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Chen S, Zhao H, Luo T, Liu Y, Nie X, Li H. Characteristics and Expression Pattern of MYC Genes in Triticum aestivum, Oryza sativa, and Brachypodium distachyon. PLANTS (BASEL, SWITZERLAND) 2019; 8:E274. [PMID: 31398900 PMCID: PMC6724133 DOI: 10.3390/plants8080274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/03/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022]
Abstract
Myelocytomatosis oncogenes (MYC) transcription factors (TFs) belong to basic helix-loop-helix (bHLH) TF family and have a special bHLH_MYC_N domain in the N-terminal region. Presently, there is no detailed and systematic analysis of MYC TFs in wheat, rice, and Brachypodium distachyon. In this study, 26 TaMYC, 7 OsMYC, and 7 BdMYC TFs were identified and their features were characterized. Firstly, they contain a JAZ interaction domain (JID) and a putative transcriptional activation domain (TAD) in the bHLH_MYC_N region and a BhlH region in the C-terminal region. In some cases, the bHLH region is followed by a leucine zipper region; secondly, they display tissue-specific expression patterns: wheat MYC genes are mainly expressed in leaves, rice MYC genes are highly expressed in stems, and B. distachyon MYC genes are mainly expressed in inflorescences. In addition, three types of cis-elements, including plant development/growth-related, hormone-related, and abiotic stresses-related were identified in different MYC gene promoters. In combination with the previous studies, these results indicate that MYC TFs mainly function in growth and development, as well as in response to stresses. This study laid a foundation for the further functional elucidation of MYC genes.
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Affiliation(s)
- Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China
| | - Hongyan Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China
| | - Tengli Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China
| | - Yue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712000, China.
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76
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Genome-Wide Analysis of Serine/Arginine-Rich Protein Family in Wheat and Brachypodium distachyon. PLANTS 2019; 8:plants8070188. [PMID: 31247888 PMCID: PMC6681277 DOI: 10.3390/plants8070188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/15/2022]
Abstract
By regulating the pre-mRNA splicing of other genes and themselves, plant serine/arginine-rich (SR) proteins play important roles in development and in response to abiotic stresses. Presently, the functions of most plant SR protein genes remain unclear. Wheat (Triticumaestivum) and Brachypodiumdistachyon are closely related species. In this study, 40 TaSR and 18 BdSR proteins were identified respectively, and they were classified into seven subfamilies: SR, RS, SCL, RSZ, RS2Z, SC35, and SR45. Similar to Arabidopsis and rice SR protein genes, most TaSR and BdSR protein genes are expressed extensively. Surprisingly, real-time polymerase chain reaction (RT-PCR) analyses showed that no alternative splicing event was found in TaSR protein genes, and only six BdSR protein genes are alternatively spliced genes. The detected alternatively spliced BdSR protein genes and transcripts are much fewer than in Arabidopsis, rice, maize, and sorghum. In the promoter regions, 92 development-related, stress-related, and hormone-related cis-elements were detected, indicating their functions in development and in response to environmental stresses. Meanwhile, 19 TaSR and 16 BdSR proteins were predicted to interact with other SR proteins or non-SR proteins, implying that they are involved in other functions in addition to modulating pre-mRNA splicing as essential components of the spliceosome. These results lay a foundation for further analyses of these genes.
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77
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Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML. Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. MOLECULAR PLANT 2019; 12:833-846. [PMID: 30953787 PMCID: PMC6557310 DOI: 10.1016/j.molp.2019.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 05/29/2023]
Abstract
Understanding how plants respond to nitrogen in their environment is crucial for determining how they use it and how the nitrogen use affects other processes related to plant growth and development. Under nitrogen limitation the activity and affinity of uptake systems is increased in roots, and lateral root formation is regulated in order to adapt to low nitrogen levels and scavenge from the soil. Plants in the legume family can form associations with rhizobial nitrogen-fixing bacteria, and this association is tightly regulated by nitrogen levels. The effect of nitrogen on nodulation has been extensively investigated, but the effects of nodulation on plant nitrogen responses remain largely unclear. In this study, we integrated molecular and phenotypic data in the legume Medicago truncatula and determined that genes controlling nitrogen influx are differently expressed depending on whether plants are mock or rhizobia inoculated. We found that a functional autoregulation of nodulation pathway is required for roots to perceive, take up, and mobilize nitrogen as well as for normal root development. Our results together revealed that autoregulation of nodulation, root development, and the location of nitrogen are processes balanced by the whole plant system as part of a resource-partitioning mechanism.
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Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Mingkee Achom
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Alonso J Pardal
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Saúl Vázquez
- Gateway Building, Sutton Bonington Campus, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Sascha Ott
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, UK
| | - John Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AH, UK; Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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78
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Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B. MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. MOLECULAR PLANT 2019; 12:879-892. [PMID: 30639314 DOI: 10.1016/j.molp.2019.01.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 01/01/2019] [Indexed: 05/18/2023]
Abstract
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
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Affiliation(s)
- Rainer Schwacke
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Gabriel Y Ponce-Soto
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, The Arctic University of Norway, Biology Building, 9037 Tromsø, Norway
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
| | - Borjana Arsova
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Asis Hallab
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Department of Systems Regulation, 14476 Potsdam-Golm, Germany
| | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany.
| | - Björn Usadel
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany; Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
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79
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Andorf C, Beavis WD, Hufford M, Smith S, Suza WP, Wang K, Woodhouse M, Yu J, Lübberstedt T. Technological advances in maize breeding: past, present and future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:817-849. [PMID: 30798332 DOI: 10.1007/s00122-019-03306-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.
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Affiliation(s)
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Matthew Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011-1010, USA
| | - Stephen Smith
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Walter P Suza
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA, 50011-1010, USA.
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80
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Yang X, Liu J, Xu J, Duan S, Wang Q, Li G, Jin L. Transcriptome Profiling Reveals Effects of Drought Stress on Gene Expression in Diploid Potato Genotype P3-198. Int J Mol Sci 2019; 20:ijms20040852. [PMID: 30781424 PMCID: PMC6413097 DOI: 10.3390/ijms20040852] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/09/2019] [Accepted: 02/13/2019] [Indexed: 01/09/2023] Open
Abstract
Potato (Solanum tuberosum L.) is one of the three most important food crops worldwide; however, it is strongly affected by drought stress. The precise molecular mechanisms of drought stress response in potato are not very well understood. The diploid potato genotype P3-198 has been verified to be highly resistant to drought stress. Here, a time-course experiment was performed to identify drought resistance response genes in P3-198 under polyethylene glycol (PEG)-induced stress using RNA-sequencing. A total of 1665 differentially expressed genes (DEGs) were specifically identified, and based on gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the transcription factor activity, protein kinase activity, and the plant hormone signal transduction process were significantly enriched. Annotation revealed that these DEGs mainly encode transcription factors, protein kinases, and proteins related to redox regulation, carbohydrate metabolism, and osmotic adjustment. In particular, genes encoding abscisic acid (ABA)-dependent signaling molecules were significantly differentially expressed, which revealed the important roles of the ABA-dependent signaling pathway in the early response of P3-198 to drought stress. Quantitative real-time PCR experimental verification confirmed the differential expression of genes in the drought resistance signaling pathway. Our results provide valuable information for understanding potato drought-resistance mechanisms, and also enrich the gene resources available for drought-resistant potato breeding.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable, Jinan 250100, China.
- National Vegetable Improvement Center Shandong Sub-Center/Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Ministry of Agriculture and Rural Affairs, Jinan 250100, China.
| | - Jie Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Jianfei Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Shaoguang Duan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Qianru Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Liping Jin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
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81
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Quezada EH, García GX, Arthikala MK, Melappa G, Lara M, Nanjareddy K. Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis. Genes (Basel) 2019; 10:genes10010059. [PMID: 30658517 PMCID: PMC6356535 DOI: 10.3390/genes10010059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/06/2019] [Accepted: 01/09/2019] [Indexed: 01/03/2023] Open
Abstract
Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the PhaseolusCRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.
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Affiliation(s)
- Elsa-Herminia Quezada
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Gabriel-Xicoténcatl García
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Govindappa Melappa
- Department of Biotechnology, Dayananda Sagar College of Engineering, Shavige Malleshwara Hills, Kumaraswamy Layout, Bengaluru 560 078, India.
| | - Miguel Lara
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), C.P. 62271 Cuernavaca, Mexico.
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
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82
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Szcześniak MW, Bryzghalov O, Ciomborowska-Basheer J, Makałowska I. CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs. Methods Mol Biol 2019; 1933:415-429. [PMID: 30945201 DOI: 10.1007/978-1-4939-9045-0_26] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of potent regulators of gene expression that are found in a wide array of eukaryotes; however, our knowledge about these molecules in plants is very limited. In particular, a number of plant species with important roles in biotechnology, agriculture and basic research still lack comprehensively identified and annotated sets of lncRNAs. To address these shortcomings, we previously created a database of lncRNAs in 10 model species, called CANTATAdb, and now we are expanding this online resource to encompass 39 species, including three algae. The lncRNAs were identified computationally using publicly available RNA sequencing (RNA-Seq) data. Expression values, coding potential calculations and other types of information were used to provide annotations for the identified lncRNAs. The data are freely available for searching, browsing and downloading from an online database called CANTATAdb 2.0 ( http://cantata.amu.edu.pl , http://yeti.amu.edu.pl/CANTATA/ ).
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Affiliation(s)
- Michał Wojciech Szcześniak
- Laboratory of Integrative Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland.
| | - Oleksii Bryzghalov
- Laboratory of Integrative Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | | | - Izabela Makałowska
- Laboratory of Integrative Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
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83
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Zhong H, Kong W, Gong Z, Fang X, Deng X, Liu C, Li Y. Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like ( SPL) Gene Family in Oryza Genus. FRONTIERS IN PLANT SCIENCE 2019; 10:565. [PMID: 31139200 PMCID: PMC6517846 DOI: 10.3389/fpls.2019.00565] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 05/07/2023]
Abstract
The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.
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84
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Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinformatics 2018; 19:534. [PMID: 30567491 PMCID: PMC6299935 DOI: 10.1186/s12859-018-2486-6] [Citation(s) in RCA: 731] [Impact Index Per Article: 121.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/12/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis. RESULTS iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses. CONCLUSIONS Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
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Affiliation(s)
- Steven Xijin Ge
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
| | - Eun Wo Son
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
| | - Runan Yao
- Department of Mathematics and Statistics, South Dakota State University, Box 2225, Brookings, SD 57007 USA
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85
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Pigolev AV, Miroshnichenko DN, Pushin AS, Terentyev VV, Boutanayev AM, Dolgov SV, Savchenko TV. Overexpression of Arabidopsis OPR3 in Hexaploid Wheat ( Triticum aestivum L.) Alters Plant Development and Freezing Tolerance. Int J Mol Sci 2018; 19:E3989. [PMID: 30544968 PMCID: PMC6320827 DOI: 10.3390/ijms19123989] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/09/2023] Open
Abstract
Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat.
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Affiliation(s)
- Alexey V Pigolev
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
| | - Dmitry N Miroshnichenko
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
| | - Alexander S Pushin
- Institute of Basic Biological Problems RAS, Pushchino 142290, Russia.
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
| | | | | | - Sergey V Dolgov
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, Pushchino 142290, Russia.
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86
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Nishiyama E, Ohshima K. Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons. Genome Biol Evol 2018; 10:1471-1483. [PMID: 29850801 PMCID: PMC6007223 DOI: 10.1093/gbe/evy098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 12/15/2022] Open
Abstract
In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.
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Affiliation(s)
- Eri Nishiyama
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
| | - Kazuhiko Ohshima
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Shiga, Japan
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87
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Nawaz MA, Lin X, Chan TF, Imtiaz M, Rehman HM, Ali MA, Baloch FS, Atif RM, Yang SH, Chung G. Characterization of Cellulose Synthase A (CESA) Gene Family in Eudicots. Biochem Genet 2018; 57:248-272. [PMID: 30267258 DOI: 10.1007/s10528-018-9888-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022]
Abstract
Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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88
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Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, Paux E, Eversole K, Adam-Blondon AF, Quesneville H. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biol 2018; 19:111. [PMID: 30115101 PMCID: PMC6097284 DOI: 10.1186/s13059-018-1491-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/23/2018] [Indexed: 01/24/2023] Open
Abstract
The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
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Affiliation(s)
- Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France.
| | - Jane Rogers
- International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge, CB23 1HE, UK
| | | | - Raphaël Flores
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | | | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Nacer Mohellibi
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Sophie Durand
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Erik Kimmel
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Célia Michotey
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Claire Guerche
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Mikaël Loaec
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Mathilde Lainé
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Delphine Steinbach
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
- Present address: GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France
| | - Frédéric Choulet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Hélène Rimbert
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Philippe Leroy
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Nicolas Guilhot
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Jérôme Salse
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Catherine Feuillet
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
- Present address: Inari Agriculture, 200 Sydney Street, Cambridge, MA, 02139, USA
| | - Etienne Paux
- GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, Maryland, 20816, USA
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89
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Gene Profiling in Late Blight Resistance in Potato Genotype SD20. Int J Mol Sci 2018; 19:ijms19061728. [PMID: 29891775 PMCID: PMC6032139 DOI: 10.3390/ijms19061728] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/18/2018] [Accepted: 06/04/2018] [Indexed: 01/05/2023] Open
Abstract
Late blight caused by the oomycete fungus Phytophthora infestans (Pi) is the most serious obstacle to potato (Solanum tuberosum) production in the world. A super race isolate, CN152, which was identified from Sichuan Province, China, could overcome nearly all known late blight resistance genes and caused serious damage in China. The potato genotype SD20 was verified to be highly resistant to CN152; however, the molecular regulation network underlying late blight resistance pathway remains unclear in SD20. Here, we performed a time-course experiment to systematically profile the late blight resistance response genes using RNA-sequencing in SD20. We identified 3354 differentially expressed genes (DEGs), which mainly encoded transcription factors and protein kinases, and also included four NBS-LRR genes. The late blight responsive genes showed time-point-specific induction/repression. Multi-signaling pathways of salicylic acid, jasmonic acid, and ethylene signaling pathways involved in resistance and defense against Pi in SD20. Gene Ontology and KEGG analyses indicated that the DEGs were significantly enriched in metabolic process, protein serine/threonine kinase activity, and biosynthesis of secondary metabolites. Forty-three DEGs were involved in immune response, of which 19 were enriched in hypersensitive response reaction, which could play an important role in broad-spectrum resistance to Pi infection. Experimental verification confirmed the induced expression of the responsive genes in the late blight resistance signaling pathway, such as WRKY, ERF, MAPK, and NBS-LRR family genes. Our results provided valuable information for understanding late blight resistance mechanism of potato.
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90
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Papatheodorou I, Fonseca NA, Keays M, Tang Y, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AMP, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res 2018; 46:D246-D251. [PMID: 29165655 PMCID: PMC5753389 DOI: 10.1093/nar/gkx1158] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/26/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022] Open
Abstract
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. Data from large-scale RNA sequencing studies including Blueprint, PCAWG, ENCODE, GTEx and HipSci can be visualized next to each other. In Expression Atlas, users can query genes or gene-sets of interest and explore their expression across or within species, tissues, developmental stages in a constitutive or differential context, representing the effects of diseases, conditions or experimental interventions. All processed data matrices are available for direct download in tab-delimited format or as R-data. In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package. Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues or other conditions.
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Affiliation(s)
- Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Maria Keays
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Y Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Elisabet Barrera
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Wojciech Bazant
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Melissa Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Laura Huerta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Satu Koskinen
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Suhaib Mohammed
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | | | | | | | - Andrew F Jarnuczak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Wolfgang Huber
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Robert Petryszak
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
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91
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Rezzonico F, Rupp O, Fahrentrapp J. Pathogen recognition in compatible plant-microbe interactions. Sci Rep 2017; 7:6383. [PMID: 28743967 PMCID: PMC5526865 DOI: 10.1038/s41598-017-04792-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/19/2017] [Indexed: 12/04/2022] Open
Abstract
Microbial infections in plant leaves remain a major challenge in agriculture. Hence an understanding of disease mechanisms at the molecular level is of paramount importance for identifying possible intervention points for their control. Whole-transcriptome changes during early disease stages in susceptible plant species are less well-documented than those of resistant ones. This study focuses on the differential transcriptional changes at 24 hours post inoculation (hpi) in tomato leaflets affected by three pathogens: (1) Phytophthora infestans, (2) Botrytis cinerea, and (3) Oidium neolycopersici. Grey mould (B. cinerea) was the disease that had progressed the most by 24 hpi, both in terms of visible symptoms as well as differential gene expression. By means of RNA-seq, we identified 50 differentially expressed tomato genes specifically induced by B. cinerea infection and 18 specifically induced by P. infestans infection at 24 hpi. Additionally, a set of 63 genes were differentially expressed during all three diseases when compared by a Bayesian approach to their respective mock infections. And Gene expression patterns were found to also depend on the inoculation technique. These findings suggest a specific and distinct transcriptional response in plant leaf tissue in reaction to B. cinerea and P. infestans invasion at 24 hpi, indicating that plants may recognize the attacking pathogen.
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Affiliation(s)
- Fabio Rezzonico
- Research Group Environmental Genomics and Systems Biology, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Johannes Fahrentrapp
- Research Group for Viticulture, Zurich University of Applied Sciences, Wädenswil, Switzerland.
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