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Aversano R, Iovene M, Esposito S, L'Abbate A, Villano C, Di Serio E, Cardone MF, Bergamini C, Cigliano RA, D'Amelia V, Frusciante L, Carputo D. Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina. BMC PLANT BIOLOGY 2024; 24:88. [PMID: 38317087 PMCID: PMC10845522 DOI: 10.1186/s12870-024-04778-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
| | - Marina Iovene
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy.
| | - Salvatore Esposito
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
- Research Centre for Cereal and Industrial Crops, Council for Agricultural Research and Economics (CREA-CI), Foggia, Italy
| | - Alberto L'Abbate
- Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy
| | - Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Ermanno Di Serio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Maria Francesca Cardone
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | - Carlo Bergamini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Turi, Italy
| | | | - Vincenzo D'Amelia
- Institute of Biosciences and Bioresources, National Research Council of Italy (CNR-IBBR), Portici, Italy
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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Li M, Wang F, Ma J, Liu H, Ye H, Zhao P, Wang J. Comprehensive Evolutionary Analysis of CPP Genes in Brassica napus L. and Its Two Diploid Progenitors Revealing the Potential Molecular Basis of Allopolyploid Adaptive Advantage Under Salt Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:873071. [PMID: 35548281 PMCID: PMC9085292 DOI: 10.3389/fpls.2022.873071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Allopolyploids exist widely in nature and have strong environmental adaptability. The typical allopolyploid Brassica napus L. is a widely cultivated crop, but whether it is superior to its diploid progenitors in abiotic stress resistance and the key genes that may be involved are not fully understood. Cystein-rich polycomb-like protein (CPP) genes encode critical transcription factors involved in the response of abiotic stress, including salt stress. To explore the potential molecular basis of allopolyploid adaptation to salt stress, we comprehensively analyzed the characteristics and salt stress response of the CPP genes in B. napus and its two diploid progenitors in this study. We found some molecular basis that might be associated with the adaptability of B. napus, including the expansion of the CPP gene family, the acquisition of introns by some BnCPPs, and abundant cis-acting elements upstream of BnCPPs. We found two duplication modes (whole genome duplication and transposed duplication) might be the main reasons for the expansion of CPP gene family in B. napus during allopolyploidization. CPP gene expression levels and several physiological indexes were changed in B. napus and its diploid progenitors after salt stress, suggesting that CPP genes might play important roles in the response of salt stress. We found that some BnCPPs might undergo new functionalization or subfunctionalization, and some BnCPPs also show biased expression, which might contribute to the adaptation of B. napus under saline environment. Compared with diploid progenitors, B. napus showed stronger physiological responses, and BnCPP gene expression also showed higher changes after salt stress, indicating that the allopolyploid B. napus had an adaptive advantage under salt stress. This study could provide evidence for the adaptability of polyploid and provide important clues for the study of the molecular mechanism of salt stress resistance in B. napus.
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Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Pépin N, Hebert FO, Joly DL. Genome-Wide Characterization of the MLO Gene Family in Cannabis sativa Reveals Two Genes as Strong Candidates for Powdery Mildew Susceptibility. FRONTIERS IN PLANT SCIENCE 2021; 12:729261. [PMID: 34589104 PMCID: PMC8475652 DOI: 10.3389/fpls.2021.729261] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Cannabis sativa is increasingly being grown around the world for medicinal, industrial, and recreational purposes. As in all cultivated plants, cannabis is exposed to a wide range of pathogens, including powdery mildew (PM). This fungal disease stresses cannabis plants and reduces flower bud quality, resulting in significant economic losses for licensed producers. The Mildew Locus O (MLO) gene family encodes plant-specific proteins distributed among conserved clades, of which clades IV and V are known to be involved in susceptibility to PM in monocots and dicots, respectively. In several studies, the inactivation of those genes resulted in durable resistance to the disease. In this study, we identified and characterized the MLO gene family members in five different cannabis genomes. Fifteen Cannabis sativa MLO (CsMLO) genes were manually curated in cannabis, with numbers varying between 14, 17, 19, 18, and 18 for CBDRx, Jamaican Lion female, Jamaican Lion male, Purple Kush, and Finola, respectively (when considering paralogs and incomplete genes). Further analysis of the CsMLO genes and their deduced protein sequences revealed that many characteristics of the gene family, such as the presence of seven transmembrane domains, the MLO functional domain, and particular amino acid positions, were present and well conserved. Phylogenetic analysis of the MLO protein sequences from all five cannabis genomes and other plant species indicated seven distinct clades (I through VII), as reported in other crops. Expression analysis revealed that the CsMLOs from clade V, CsMLO1 and CsMLO4, were significantly upregulated following Golovinomyces ambrosiae infection, providing preliminary evidence that they could be involved in PM susceptibility. Finally, the examination of variation within CsMLO1 and CsMLO4 in 32 cannabis cultivars revealed several amino acid changes, which could affect their function. Altogether, cannabis MLO genes were identified and characterized, among which candidates potentially involved in PM susceptibility were noted. The results of this study will lay the foundation for further investigations, such as the functional characterization of clade V MLOs as well as the potential impact of the amino acid changes reported. Those will be useful for breeding purposes in order to develop resistant cultivars.
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Affiliation(s)
- Noémi Pépin
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
| | - Francois Olivier Hebert
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
- Institut National des Cannabinoïdes, Montréal, QC, Canada
| | - David L. Joly
- Centre d’Innovation et de Recherche sur le Cannabis, Université de Moncton, Département de biologie, Moncton, NB, Canada
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Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC. Deeply Altered Genome Architecture in the Endoparasitic Flowering Plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol 2021; 31:1002-1011.e9. [DOI: 10.1016/j.cub.2020.12.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/11/2020] [Accepted: 12/23/2020] [Indexed: 12/18/2022]
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Mukherjee D, Saha D, Acharya D, Mukherjee A, Chakraborty S, Ghosh TC. The role of introns in the conservation of the metabolic genes of Arabidopsis thaliana. Genomics 2018; 110:310-317. [DOI: 10.1016/j.ygeno.2017.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
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García-Gutiérrez Á, Cánovas FM, Ávila C. Glutamate synthases from conifers: gene structure and phylogenetic studies. BMC Genomics 2018; 19:65. [PMID: 29351733 PMCID: PMC5775586 DOI: 10.1186/s12864-018-4454-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/15/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants. In conifers, partial cDNA sequences for GOGATs have been isolated and used for gene expression studies. However, knowledge of the gene structure and of phylogenetic relationships with other plant enzymes is quite scant. RESULTS Technological advances in conifer megagenomes sequencing have made it possible to obtain full-length cDNA sequences encoding Fd- and NADH-GOGAT from maritime pine, as well as BAC clones containing sequences for NADH-GOGAT and Fd-GOGAT genes. In the current study, we studied the genomic organization of pine GOGAT genes, the size of their exons/introns, copy numbers in the pine genome and relationships with other plant genes. Phylogenetic analysis was performed, and the degree of preservation and dissimilarity of key domains for the catalytic activities of these enzymes in different taxa were determined. CONCLUSIONS Fd- and NADH-GOGAT are encoded by single-copy genes in the maritime pine genome. The Fd-GOGAT gene is extremely large spanning more than 330 kb and the presence of very long introns highlights the important contribution of LTR retrotransposons to the gene size in conifers. In contrast, the structure of the NADH-GOGAT gene is similar to the orthologous genes in angiosperms. Our phylogenetic analysis indicates that these two genes had different origins during plant evolution. The results provide new insights into the structure and molecular evolution of these essential genes.
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Affiliation(s)
- Ángel García-Gutiérrez
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Francisco M. Cánovas
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Concepción Ávila
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
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Gavazzi F, Braglia L, Mastromauro F, Gianì S, Morello L, Breviario D. The Tubulin-Based-Polymorphism Method Provides a Simple and Effective Alternative to the Genomic Profiling of Grape. PLoS One 2016; 11:e0163335. [PMID: 27643687 PMCID: PMC5028034 DOI: 10.1371/journal.pone.0163335] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
The TBP (Tubulin-Based-Polymorphism) method, based on a nuclear ILP (Intron-Length-Polymorphism) molecular marker, has been used for genotyping 37 accessions of the genus Vitis inclusive of different species, rootstocks, wild and cultivated subspecies. A distinct DNA barcode made up by a different number of amplicons, was attributed to each of the different accessions. TBP data were compared with those obtained, with the use of an internationally validated set of six SSR markers. Genetic relationships among the different accessions, dendrogram distributions, correlation values and polymorphic index values (PICs) were definitively comparable when not in favor of TBP. Such an experimental consistency is based upon a genomic organization of the multiple members of the β-tubulin gene family, the targets of TBP-mediated amplification, that is conserved in Vitis as in any other plant species. The TBP amplicons can actually be used as a useful source of sequence polymorphisms for generating primer pairs capable of identifying specific cultivars in a simple assay. An example for the identification of the ‘Sangiovese’ cv. is reported. More generally, these data are discussed in terms of the actual advantages that the introduction of the TBP method in the field of grape characterization and genotyping can provide.
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Affiliation(s)
- Floriana Gavazzi
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
| | - Luca Braglia
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
| | - Francesco Mastromauro
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
| | - Silvia Gianì
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
| | - Laura Morello
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
| | - Diego Breviario
- Institute of Agricultural Biology and Biotechnology - National Research Council, Milan, Italy
- * E-mail:
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Evolutionary characterization of Ty3/gypsy-like LTR retrotransposons in the parasitic cestode Echinococcus granulosus. Parasitology 2016; 143:1691-1702. [PMID: 27571603 DOI: 10.1017/s0031182016001499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.
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Abstract
In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Scott William Roy
- Department of Biology, San Francisco State University, San Francisco, California 94132
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Stival Sena J, Giguère I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, Bousquet J, Mackay J. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC PLANT BIOLOGY 2014; 14:95. [PMID: 24734980 PMCID: PMC4108047 DOI: 10.1186/1471-2229-14-95] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/09/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described. RESULTS Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons. CONCLUSION Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles.
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Affiliation(s)
- Juliana Stival Sena
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Isabelle Giguère
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Brian Boyle
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | | | - Inanc Birol
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrea Zuccolo
- Applied Genomics Institute, Udine 33100, Italy
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
| | - Kermit Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carol Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Steven Jones
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, Université Laval, Québec, QC G1V 0A6, Canada
| | - John Mackay
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
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Molina-Rueda JJ, Tsai CJ, Kirby EG. The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a). PLoS One 2013; 8:e56421. [PMID: 23451045 PMCID: PMC3579828 DOI: 10.1371/journal.pone.0056421] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/09/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Glutamine synthetase (GS) plays a central role in plant nitrogen assimilation, a process intimately linked to soil water availability. We previously showed that hybrid poplar (Populus tremula X alba, INRA 717-1B4) expressing ectopically a pine cytosolic glutamine synthetase gene (GS1a) display enhanced tolerance to drought. Preliminary transcriptome profiling revealed that during drought, members of the superoxide dismutase (SOD) family were reciprocally regulated in GS poplar when compared with the wild-type control, in all tissues examined. SOD was the only gene family found to exhibit such patterns. RESULTS In silico analysis of the Populus genome identified 12 SOD genes and two genes encoding copper chaperones for SOD (CCSs). The poplar SODs form three phylogenetic clusters in accordance with their distinct metal co-factor requirements and gene structure. Nearly all poplar SODs and CCSs are present in duplicate derived from whole genome duplication, in sharp contrast to their predominantly single-copy Arabidopsis orthologs. Drought stress triggered plant-wide down-regulation of the plastidic copper SODs (CSDs), with concomitant up-regulation of plastidic iron SODs (FSDs) in GS poplar relative to the wild type; this was confirmed at the activity level. We also found evidence for coordinated down-regulation of other copper proteins, including plastidic CCSs and polyphenol oxidases, in GS poplar under drought conditions. CONCLUSIONS Both gene duplication and expression divergence have contributed to the expansion and transcriptional diversity of the Populus SOD/CCS families. Coordinated down-regulation of major copper proteins in drought-tolerant GS poplars supports the copper cofactor economy model where copper supply is preferentially allocated for plastocyanins to sustain photosynthesis during drought. Our results also extend previous findings on the compensatory regulation between chloroplastic CSDs and FSDs, and suggest that this copper-mediated mechanism represents a common response to oxidative stress and other genetic manipulations, as in GS poplars, that affect photosynthesis.
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Affiliation(s)
- Juan Jesús Molina-Rueda
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, United States of America
| | - Chung Jui Tsai
- Warnell School of Forestry and Natural Resources and Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Edward G. Kirby
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, United States of America
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