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Schmidt N, Sielemann K, Breitenbach S, Fuchs J, Pucker B, Weisshaar B, Holtgräwe D, Heitkam T. Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:171-190. [PMID: 38128038 DOI: 10.1111/tpj.16599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Sarah Breitenbach
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Graz, Austria
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2
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Ponvert N, Johnson MA. Synergid cell calcium oscillations refine understanding of FERONIA/LORELEI signaling during interspecific hybridization. PLANT REPRODUCTION 2024; 37:57-68. [PMID: 37934279 PMCID: PMC10879309 DOI: 10.1007/s00497-023-00483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
KEY MESSAGE Pollen tubes from closely related species and mutants lacking pollen tube MYB transcription factors are able to initiate FER/LRE-dependent synergid cell calcium oscillations. Reproductive isolation leads to the evolution of new species; however, the molecular mechanisms that maintain reproductive barriers between sympatric species are not well defined. In flowering plants, sperm cells are immotile and are delivered to female gametes by the pollen grain. After landing on the stigmatic surface, the pollen grain germinates a polarized extension, the pollen tube, into floral tissue. After growing via polar extension to the female gametes and shuttling its cargo of sperm cells through its cytoplasm, the pollen tube signals its arrival and identity to synergid cells that flank the egg. If signaling is successful, the pollen tube and receptive synergid cell burst, and sperm cells are released for fusion with female gametes. To better understand cell-cell recognition during reproduction and how reproductive barriers are maintained between closely related species, pollen tube-initiated synergid cell calcium ion dynamics were examined during interspecific crosses. It was observed that interspecific pollen tubes successfully trigger synergid cell calcium oscillations-a hallmark of reproductive success-but signaling fails downstream of key signaling genes and sperm are not released. This work further defines pollen tube-synergid cell signaling as a critical block to interspecific hybridization and suggests that the FERONIA/LORELEI signaling mechanism plays multiple parallel roles during pollen tube reception.
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Affiliation(s)
- Nathaniel Ponvert
- Department of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Mark A Johnson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.
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Marchetti M, Piacentini L, Berloco MF, Casale AM, Cappucci U, Pimpinelli S, Fanti L. Cytological heterogeneity of heterochromatin among 10 sequenced Drosophila species. Genetics 2022; 222:iyac119. [PMID: 35946576 PMCID: PMC9526073 DOI: 10.1093/genetics/iyac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/14/2022] Open
Abstract
In Drosophila chromosomal rearrangements can be maintained and are associated with karyotypic variability among populations from different geographic localities. The abundance of variability in gene arrangements among chromosomal arms is even greater when comparing more distantly related species and the study of these chromosomal changes has provided insights into the evolutionary history of species in the genus. In addition, the sequencing of genomes of several Drosophila species has offered the opportunity to establish the global pattern of genomic evolution, at both genetic and chromosomal level. The combined approaches of comparative analysis of syntenic blocks and direct physical maps on polytene chromosomes have elucidated changes in the orientation of genomic sequences and the difference between heterochromatic and euchromatic regions. Unfortunately, the centromeric heterochromatic regions cannot be studied using the cytological maps of polytene chromosomes because they are underreplicated and therefore reside in the chromocenter. In Drosophila melanogaster, a cytological map of the heterochromatin has been elaborated using mitotic chromosomes from larval neuroblasts. In the current work, we have expanded on that mapping by producing cytological maps of the mitotic heterochromatin in an additional 10 sequenced Drosophila species. These maps highlight 2 apparently different paths, for the evolution of the pericentric heterochromatin between the subgenera Sophophora and Drosophila. One path leads toward a progressive complexity of the pericentric heterochromatin (Sophophora) and the other toward a progressive simplification (Drosophila). These maps are also useful for a better understanding how karyotypes have been altered by chromosome arm reshuffling during evolution.
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Affiliation(s)
- Marcella Marchetti
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Lucia Piacentini
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
| | | | - Assunta Maria Casale
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Ugo Cappucci
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Sergio Pimpinelli
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
| | - Laura Fanti
- Istituto Pasteur Italia and Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” University of Rome, 00185 Rome, Italy
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Huang Y, Chen J, Dong C, Sosa D, Xia S, Ouyang Y, Fan C, Li D, Mortola E, Long M, Bergelson J. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. THE PLANT CELL 2022; 34:802-817. [PMID: 34875081 PMCID: PMC8824575 DOI: 10.1093/plcell/koab291] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/25/2021] [Indexed: 05/04/2023]
Abstract
Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-sequencing analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana.
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Affiliation(s)
- Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Jiahui Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chuan Dong
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Dezhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Emily Mortola
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
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Kadluczka D, Grzebelus E. Using carrot centromeric repeats to study karyotype relationships in the genus Daucus (Apiaceae). BMC Genomics 2021; 22:508. [PMID: 34225677 PMCID: PMC8259371 DOI: 10.1186/s12864-021-07853-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/24/2021] [Indexed: 01/01/2023] Open
Abstract
Background In the course of evolution, chromosomes undergo evolutionary changes; thus, karyotypes may differ considerably among groups of organisms, even within closely related taxa. The genus Daucus seems to be a promising model for exploring the dynamics of karyotype evolution. It comprises some 40 wild species and the cultivated carrot, a crop of great economic significance. However, Daucus species are very diverse morphologically and genetically, and despite extensive research, the taxonomic and phylogenetic relationships between them have still not been fully resolved. Although several molecular cytogenetic studies have been conducted to investigate the chromosomal structure and karyotype evolution of carrot and other Daucus species, detailed karyomorphological research has been limited to carrot and only a few wild species. Therefore, to better understand the karyotype relationships within Daucus, we (1) explored the chromosomal distribution of carrot centromeric repeats (CentDc) in 34 accessions of Daucus and related species by means of fluorescence in situ hybridization (FISH) and (2) performed detailed karyomorphological analysis in 16 of them. Results We determined the genomic organization of CentDc in 26 accessions of Daucus (belonging to both Daucus I and II subclades) and one accession of closely related species. The CentDc repeats were present in the centromeric regions of all chromosomes of 20 accessions (representing 11 taxa). In the other Daucus taxa, the number of chromosome pairs with CentDc signals varied depending on the species, yet their centromeric localization was conserved. In addition, precise chromosome measurements performed in 16 accessions showed the inter- and intraspecific karyological relationships among them. Conclusions The presence of the CentDc repeats in the genomes of taxa belonging to both Daucus subclades and one outgroup species indicated the ancestral status of the repeat. The results of our study provide useful information for further evolutionary, cytotaxonomic, and phylogenetic research on the genus Daucus and may contribute to a better understanding of the dynamic evolution of centromeric satellites in plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07853-2.
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Affiliation(s)
- Dariusz Kadluczka
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, al. 29 Listopada 54, 31-425, Krakow, Poland.
| | - Ewa Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, al. 29 Listopada 54, 31-425, Krakow, Poland.
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Angulo-Bejarano PI, Puente-Rivera J, Cruz-Ortega R. Metal and Metalloid Toxicity in Plants: An Overview on Molecular Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:635. [PMID: 33801570 PMCID: PMC8066251 DOI: 10.3390/plants10040635] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022]
Abstract
Worldwide, the effects of metal and metalloid toxicity are increasing, mainly due to anthropogenic causes. Soil contamination ranks among the most important factors, since it affects crop yield, and the metals/metalloids can enter the food chain and undergo biomagnification, having concomitant effects on human health and alterations to the environment. Plants have developed complex mechanisms to overcome these biotic and abiotic stresses during evolution. Metals and metalloids exert several effects on plants generated by elements such as Zn, Cu, Al, Pb, Cd, and As, among others. The main strategies involve hyperaccumulation, tolerance, exclusion, and chelation with organic molecules. Recent studies in the omics era have increased knowledge on the plant genome and transcriptome plasticity to defend against these stimuli. The aim of the present review is to summarize relevant findings on the mechanisms by which plants take up, accumulate, transport, tolerate, and respond to this metal/metalloid stress. We also address some of the potential applications of biotechnology to improve plant tolerance or increase accumulation.
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Affiliation(s)
- Paola I. Angulo-Bejarano
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
- School of Engineering and Sciences, Centre of Bioengineering, Tecnologico de Monterrey, Queretaro 21620, Mexico
| | - Jonathan Puente-Rivera
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
| | - Rocío Cruz-Ortega
- Laboratorio de Alelopatía, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, UNAM, 275, Ciudad Universitaria D.F. Circuito Exterior s/n Anexo al Jardín Botánico Exterior, México City 04510, Mexico; (P.I.A.-B.); (J.P.-R.)
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Ferraz ME, Fonsêca A, Pedrosa-Harand A. Multiple and independent rearrangements revealed by comparative cytogenetic mapping in the dysploid Leptostachyus group (Phaseolus L., Leguminosae). Chromosome Res 2020; 28:395-405. [PMID: 33191473 DOI: 10.1007/s10577-020-09644-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 10/23/2022]
Abstract
Polyploidy and dysploidy have been reported as the main events in karyotype evolution of plants. In the genus Phaseolus L. (2n = 22), a small monophyletic group of three species, the Leptostachyus group, presents a dysploid karyotype with 2n = 20. It was shown in Phaseolus leptostachyus that the dysploidy was caused by a nested chromosome fusion (NCF) accompanied by several translocations, suggesting a high rate of karyotype evolution in the group. To verify if this karyotype restructuring was a single event or occurred progressively during the evolution of this group, we analysed P. macvaughii, sister to Phaseolus micranthus + P. leptostachyus. Twenty-four genomic clones of P. vulgaris previously mapped on P. leptostachyus, in addition to the 5S and 35S rDNA probes, were used for fluorescence in situ hybridization. Only a single rearrangement was common to the two species: the nested chromosome fusion (NCF) involving chromosomes 10 and 11. The translocation of chromosome 2 is not the same found in P. leptostachyus, and pericentric inversions in chromosomed 3 and 4 were exclusive of P. macvaughii. The other rearrangements observed in P. leptostachyus were not shared with this species, suggesting that they occurred after the separation of these lineages. The presence of private rearrangements indicates a progressive accumulation of karyotype changes in the Leptostachyus group instead of an instant genome-wide repatterning.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Artur Fonsêca
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil
| | - Andrea Pedrosa-Harand
- Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco - UFPE, R. Prof. Moraes Rego, s/n, CDU, Recife, PE, 50670-420, Brazil.
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Rolling Circle Amplification (RCA)-Mediated Genome-Wide ihpRNAi Mutant Library Construction in Brassica napus. Int J Mol Sci 2020; 21:ijms21197243. [PMID: 33008068 PMCID: PMC7582411 DOI: 10.3390/ijms21197243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
With the successful completion of genomic sequencing for Brassica napus, identification of novel genes, determination of functions performed by genes, and exploring the molecular mechanisms underlying important agronomic traits were challenged. Mutagenesis-based functional genomics techniques including chemical, physical, and insertional mutagenesis have been used successfully in the functional characterization of genes. However, these techniques had their disadvantages and inherent limitations for allopolyploid Brassica napus, which contained a large number of homologous and redundant genes. Long intron-spliced hairpin RNA (ihpRNA) constructs which contained inverted repeats of the target gene separated by an intron, had been shown to be very effective in triggering RNAi in plants. In the present study, the genome-wide long ihpRNA library of B. napus was constructed with the rolling circle amplification (RCA)-mediated technology. Using the phytoene desaturase (PDS) gene as a target control, it was shown that the RCA-mediated long ihpRNA construct was significantly effective in triggering gene silence in B. napus. Subsequently, the resultant long ihpRNA library was transformed into B. napus to produce corresponding RNAi mutants. Among the obtained transgenic ihpRNA population of B. napus, five ihpRNA lines with observable mutant phenotypes were acquired including alterations in the floral model and the stamen development. The target genes could be quickly identified using specific primers. These results showed that the RCA-mediated ihpRNA construction method was effective for the genome-wide long ihpRNA library of B. napus, therefore providing a platform for study of functional genomics in allopolyploid B. napus.
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Geleta M, Gustafsson C, Glaubitz JC, Ortiz R. High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes. FRONTIERS IN PLANT SCIENCE 2020; 11:448. [PMID: 32425961 PMCID: PMC7204607 DOI: 10.3389/fpls.2020.00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1-Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.
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Affiliation(s)
- Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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10
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Ostevik KL, Samuk K, Rieseberg LH. Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower. Genetics 2020; 214:1031-1045. [PMID: 32033968 PMCID: PMC7153943 DOI: 10.1534/genetics.120.303026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
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Affiliation(s)
- Kate L Ostevik
- Department of Biology, Duke University, Durham, North Carolina 27701
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kieran Samuk
- Department of Biology, Duke University, Durham, North Carolina 27701
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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11
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 DOI: 10.3389/fpls.2020.00296/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/24/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 PMCID: PMC7093584 DOI: 10.3389/fpls.2020.00296] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/11/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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13
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Delprat A, Guillén Y, Ruiz A. Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage. J Hered 2020; 110:102-117. [PMID: 30407542 DOI: 10.1093/jhered/esy057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/03/2018] [Indexed: 12/27/2022] Open
Abstract
We investigated rates of chromosomal evolution in Drosophila mojavensis using whole-genome sequence information from D. mojavensis, Drosophila buzzatii, and Drosophila virilis. Drosophila mojavensis is a cactophilic species of the repleta group living under extreme ecological conditions in the deserts of the Southwestern United States and Northwestern México. The genome of D. buzzatii, another member of the repleta group, was recently sequenced and the largest scaffolds anchored to all chromosomes using diverse procedures. Chromosome organization between D. mojavensis and D. buzzatii was compared using MUMmer and GRIMM software. Our results corroborate previous cytological analyses that indicated chromosome 2 differed between these 2 species by 10 inversions, chromosomes X and 5 differed by one inversion each, and chromosome 4 was homosequential. In contrast, we found that chromosome 3 differed by 5 inversions instead of the expected 2 that were previously inferred by cytological analyses. Thirteen of these inversions occurred in the D. mojavensis lineage: 12 are fixed and one of them is a polymorphic inversion previously described in populations from Sonora and Baja California, México. We previously investigated the breakpoints of chromosome 2 inversions fixed in D. mojavensis. Here we characterized the breakpoint regions of the 5 inversions found in chromosome 3 in order to infer the molecular mechanism that generated each inversion and its putative functional consequences. Overall, our results reveal a number of gene alterations at the inversion breakpoints with putative adaptive consequences that point to natural selection as the cause for fast chromosomal evolution in D. mojavensis.
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Affiliation(s)
- Alejandra Delprat
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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14
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Xiao L, Li X, Liu F, Zhao Z, Xu L, Chen C, Wang Y, Shang G, Du D. Mutations in the CDS and promoter of BjuA07.CLV1 cause a multilocular trait in Brassica juncea. Sci Rep 2018; 8:5339. [PMID: 29593311 PMCID: PMC5871799 DOI: 10.1038/s41598-018-23636-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/15/2018] [Indexed: 11/13/2022] Open
Abstract
Multilocular trait has recently attracted considerable attention for its potential to increase yield. Our previous studies indicated that two genes (Bjln1 and Bjln2) are responsible for multilocular siliques in Brassica juncea and the Bjln1 gene has been delimited to a 208-kb region. In present study, the Bjln1 gene was successfully isolated using the map-based cloning method. Complementation test indicated that the BjuA07.CLV1 (equivalent to BjLn1) could rescue the multilocular phenotype and generate bilocular siliques. Two amino acids changes at positions 28 and 63 in BjuA07.clv1 as well as a 702-bp deletion in its promoter have been proved to affect the carpel numbers. Microscopic analyses suggested that BjuA07.CLV1 is involved in the maintenance of shoot and floral meristem size. The expression level of BjuA07.clv1 was significantly reduced in the SAM. Furthermore, WUS, CLV2, CLV3, RPK2 and POL, key genes in the CLV/WUS signal pathway, showed lower expression level in the multilocular plants. These data suggest that the mutations in the CDS and promoter of BjuA07.clv1 reduced its function and expression level, which disturbed CLV/WUS signal pathway, thereby leading to the enlargement of the shoot and floral meristem and resulting in the multilocular siliques.
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Affiliation(s)
- Lu Xiao
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Xin Li
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Fei Liu
- National Key Lab of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zhi Zhao
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Liang Xu
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Cuiping Chen
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Yanhua Wang
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Guoxia Shang
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Dezhi Du
- State Key Laboratory of Plateau Ecology and Agriculture of Qinghai University, Key Laboratory of Qinghai Province for Spring Rapeseed Genetic Improvement, The Qinghai Research Branch of the National Rapeseed Genetic Improvement Center, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China.
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15
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A naturally occurring epiallele associates with leaf senescence and local climate adaptation in Arabidopsis accessions. Nat Commun 2018; 9:460. [PMID: 29386641 PMCID: PMC5792623 DOI: 10.1038/s41467-018-02839-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Epigenetic variation has been proposed to facilitate adaptation to changing environments, but evidence that natural epialleles contribute to adaptive evolution has been lacking. Here we identify a retrotransposon, named “NMR19” (naturally occurring DNA methylation variation region 19), whose methylation and genomic location vary among Arabidopsis thaliana accessions. We classify NMR19 as NMR19-4 and NMR19-16 based on its location, and uncover NMR19-4 as an epiallele that controls leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH). We find that the DNA methylation status of NMR19-4 is stably inherited and independent of genetic variation. In addition, further analysis indicates that DNA methylation of NMR19-4 correlates with local climates, implying that NMR19-4 is an environmentally associated epiallele. In summary, we discover a novel epiallele, and provide mechanistic insights into its origin and potential function in local climate adaptation. Epigenetic variation underlies various aspects of phenotypic diversity of plants. Here, He et al show a naturally occurring epiallele controls Arabidopsis leaf senescence by regulating the expression of PHEOPHYTIN PHEOPHORBIDE HYDROLASE (PPH), and is associated with local climate adaptation.
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16
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Merlot S, Sanchez Garcia de la Torre V, Hanikenne M. Physiology and Molecular Biology of Trace Element Hyperaccumulation. AGROMINING: FARMING FOR METALS 2018. [DOI: 10.1007/978-3-319-61899-9_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants. Genes (Basel) 2017; 8:genes8100290. [PMID: 29064432 PMCID: PMC5664140 DOI: 10.3390/genes8100290] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/18/2023] Open
Abstract
Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.
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18
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Wang Y, Li Y, Suo Y, Min Y, Kang X. Proteomic Changes Between Populus Allotriploids and Diploids Revealed Using an iTRAQ-based Quantitative Approach. CURR PROTEOMICS 2017; 14:166-174. [PMID: 29151823 PMCID: PMC5676023 DOI: 10.2174/1570164614666170310142405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/20/2017] [Accepted: 03/02/2017] [Indexed: 12/16/2022]
Abstract
Background Polyploid breeding is a powerful approach for Populus genetic improve-ment because polyploid trees have valuable characteristics, including better timber quality and a higher degree of stress resistance compared with their full-sib diploids. However, the genetic mech-anism underlying this phenomenon remains unknown. Objective To better understand the proteomic changes between Populus allotriploids and diploids, we examined the proteomic profiles of allotriploid and diploid Populus by iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS). Method iTRAQ labeling coupled with two-dimensional liquid chromatography and MALDI-TOF/TOF mass spectrometry (MS). Results Between the Populus allotriploid and the full-sib diploid, 932 differentially expressed proteins (DEPs) were identified. These DEPs were primarily involved in stress, defense, transportation, transcriptional and/or translational modification, and energy production. The pathway analysis indi-cated that most of the DEPs were implicated in carbohydrate transport and metabolism, nitrogen me-tabolism and glycolysis, and the ribosome assembly pathway. These data suggest high protein di-vergence between Populus allotriploids and diploids, and rapid changes during hybridization. Conclusion The results provide new data for further understanding of the mechanisms of polyploid trees that generally display increased height growth compared with their full-sib diploids.
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Affiliation(s)
- Yi Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China
| | - Yujing Suo
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China
| | - Yu Min
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China
| | - Xiangyang Kang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China.,Beijing Laboratory of Urban and Rural Ecological Environment, Beijing Forestry University, No. 35, Qinghua East Road, Beijing100083, China
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19
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Schouten HJ, Vande Geest H, Papadimitriou S, Bemer M, Schaart JG, Smulders MJM, Perez GS, Schijlen E. Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere. PLANT CELL REPORTS 2017; 36:493-504. [PMID: 28155116 PMCID: PMC5316556 DOI: 10.1007/s00299-017-2098-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/02/2017] [Indexed: 05/05/2023]
Abstract
KEY MESSAGE Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.
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Affiliation(s)
- Henk J Schouten
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Henri Vande Geest
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sofia Papadimitriou
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marian Bemer
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan G Schaart
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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20
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Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, Croteau RB, Straub SCK, Pandelova I, Lange BM. Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. MOLECULAR PLANT 2017; 10:323-339. [PMID: 27867107 DOI: 10.1016/j.molp.2016.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/28/2016] [Accepted: 10/29/2016] [Indexed: 05/08/2023]
Abstract
The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L.) Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb genome contains 35 597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1397 genome scaffolds on 12 pseudochromosomes. More than two million simple sequence repeats were identified, which will facilitate molecular marker development. The M. longifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize the promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA.
| | - Sean R Johnson
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amirhossein Ahkami
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Susan C Trapp
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B Croteau
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - B Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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21
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Xia S, Wang Z, Zhang H, Hu K, Zhang Z, Qin M, Dun X, Yi B, Wen J, Ma C, Shen J, Fu T, Tu J. Altered Transcription and Neofunctionalization of Duplicated Genes Rescue the Harmful Effects of a Chimeric Gene in Brassica napus. THE PLANT CELL 2016; 28:2060-2078. [PMID: 27559024 PMCID: PMC5059798 DOI: 10.1105/tpc.16.00281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/19/2016] [Accepted: 08/24/2016] [Indexed: 05/04/2023]
Abstract
Chimeric genes contribute to the evolution of diverse functions in plants and animals. However, new chimeric genes also increase the risk of developmental defects. Here, we show that the chimeric gene Brassica napus male sterile 4 (Bnams4b ) is responsible for genic male sterility in the widely used canola line 7365A (Bnams3 ms3ms4bms4b ). Bnams4b originated via exon shuffling ∼4.6 million years ago. It causes defects in the normal functions of plastids and induces aborted anther formation and/or albino leaves and buds. Evidence of the age of the mutation, its tissue expression pattern, and its sublocalization indicated that it coevolved with BnaC9.Tic40 (BnaMs3). In Arabidopsis thaliana, Bnams4b results in complete male sterility that can be rescued by BnaC9.Tic40, suggesting that BnaC9.Tic40 might restore fertility through effects on protein level. Another suppressor gene, Bnams4a , rescues sterility by reducing the level of transcription of Bnams4b Our results suggest that Brassica plants have coevolved altered transcription patterns and neofunctionalization of duplicated genes that can block developmental defects resulting from detrimental chimeric genes.
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Affiliation(s)
- Shengqian Xia
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixin Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiyan Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaining Hu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiqiang Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Maomao Qin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoling Dun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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22
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Rathore P, Geeta R, Das S. Microsynteny and phylogenetic analysis of tandemly organised miRNA families across five members of Brassicaceae reveals complex retention and loss history. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 247:35-48. [PMID: 27095398 DOI: 10.1016/j.plantsci.2016.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/04/2016] [Accepted: 03/05/2016] [Indexed: 06/05/2023]
Abstract
Plant genomes are characterized by the presence of large miRNA gene families which are few in number. The expansion of miRNA families is thought to be driven by gene and genome duplication. Some members of these miRNA gene families are tandemly arranged and their analysis is of interest because such organisation may indicate origin through tandem duplication and also to investigate whether some such tandem clusters have similar expression patterns, and whether these are regulated through a common set of cis-regulatory elements (eg. promoters and enhancers). As a first step, we undertake a comprehensive study using micro-synteny analyses of tandemly organised miRNA families across the Brassicaceae spanning an evolutionary time scale of ca. 45 million years, among Arabidopsis, Capsella, Brassica and Thellungiella species, to address the following questions: Are most miRNA gene families present as tandem clusters? To what extent are these tandem patterns retained? To what extent can family sizes be ascribed to genome duplication? Our analysis of thirteen tandemly organised miRNA families revealed that synteny is largely conserved among Arabidopsis thaliana, A. lyrata and Capsella rubella, which form a clade spanning approximately between 6.2-9.8 my (Acarkan et al., 2000) [1]. On the other hand, comparison of sequences from these species with Brassica rapa, B. oleracea and Thellungiella halophila, which form a separate clade spanning 31 my (Franzke et al., 2011)[2] reveals many differences. The latter clade reveals several paralogous duplications that probably resulted from whole genome duplication, as well as disrupted synteny. Phylogenetic analyses of precursor sequences generally support the history inferred from synteny analysis. Synteny and phylogenetic analysis of six members of the tandemly organised miR169 family suggest that the Brassicaceae ancestral state consisted of a "dimer as a unit" which may have undergone direct local duplication to retain the transcriptional orientation followed by lineage specific changes. MiR169, to the best of our knowledge, is one of the largest tandemly organised miRNA gene family across plant kingdom and further analysis should reveal the generality of this pattern of evolution. The conserved organisation of miR395A-B-C and miR395 D-E-F as two clusters on same chromosome/scaffold across A. thaliana, B. rapa and salsuginea demonstrates retention of the large chromosomal segment across the two lineages. MiRNA family miR845 was detected only in Arabidopsis species and Thellungiella indicating a complex loss and retention history. MiR447A-B family was only found in A. thaliana indicating that it is a species-specific gene family of recent origin.
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Affiliation(s)
| | - R Geeta
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi 110007, India.
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Rockinger A, Sousa A, Carvalho FA, Renner SS. Chromosome number reduction in the sister clade of Carica papaya with concomitant genome size doubling. AMERICAN JOURNAL OF BOTANY 2016; 103:1082-8. [PMID: 27234227 DOI: 10.3732/ajb.1600134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/03/2016] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY Caricaceae include six genera and 34 species, among them papaya, a model species in plant sex chromosome research. The family was held to have a conserved karyotype with 2n = 18 chromosomes, an assumption based on few counts. We examined the karyotypes and genome size of species from all genera to test for possible cytogenetic variation. METHODS We used fluorescent in situ hybridization using standard telomere, 5S, and 45S rDNA probes. New and published data were combined with a phylogeny, molecular clock dating, and C values (available for ∼50% of the species) to reconstruct genome evolution. KEY RESULTS The African genus Cylicomorpha, which is sister to the remaining Caricaceae (all neotropical), has 2n = 18, as do the species in two other genera. A Mexican clade of five species that includes papaya, however, has 2n = 18 (papaya), 2n = 16 (Horovitzia cnidoscoloides), and 2n = 14 (Jarilla caudata and J. heterophylla; third Jarilla not counted), with the phylogeny indicating that the dysploidy events occurred ∼16.6 and ∼5.5 million years ago and that Jarilla underwent genome size doubling (∼450 to 830-920 Mbp/haploid genome). Pericentromeric interstitial telomere repeats occur in both Jarilla adjacent to 5S rDNA sites, and the variability of 5S rDNA sites across all genera is high. CONCLUSIONS On the basis of outgroup comparison, 2n = 18 is the ancestral number, and repeated chromosomal fusions with simultaneous genome size increase as a result of repetitive elements accumulating near centromeres characterize the papaya clade. These results have implications for ongoing genome assemblies in Caricaceae.
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Affiliation(s)
| | - Aretuza Sousa
- Systematic Botany and Mycology, University of Munich, 80638 Munich, Germany
| | | | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich, 80638 Munich, Germany
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Jain A, Das S. Synteny and comparative analysis of miRNA retention, conservation, and structure across Brassicaceae reveals lineage- and sub-genome-specific changes. Funct Integr Genomics 2016; 16:253-68. [PMID: 26873704 DOI: 10.1007/s10142-016-0484-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 12/22/2022]
Abstract
The recent availability of genome sequences together with syntenic block information for Brassicaceae offers an opportunity to study microRNA (miRNA) evolution across this family. We employed a synteny-based comparative genomics strategy to unambiguously identify miRNA homologs from the genome sequence of members of Brassicaceae. Such an analysis of miRNA across Brassicaceae allowed us to classify miRNAs as conserved, lineage-, karyotype- and sub-genome-specific. The differential loss of miRNA from sub-genomes in polyploid genomes of Brassica rapa and Brassica oleracea shows that miRNA also follows the rules of gene fractionation as observed in the case of protein-coding genes. The study of mature and miR* region of precursors revealed instances of in-dels and SNPs which reflect the evolutionary history of the genomes. High level of conservation in miR* regions in some cases points to their functional relevance which needs to be further investigated. We further show that sequence and length variability in precursor sequences can affect the free energy and foldback structure of miRNA which may ultimately affect their biogenesis and expression in the biological system.
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Affiliation(s)
- Aditi Jain
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, Faculty of Science, University of Delhi, New Delhi, Delhi, 110007, India.
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Nouet C, Charlier JB, Carnol M, Bosman B, Farnir F, Motte P, Hanikenne M. Functional analysis of the three HMA4 copies of the metal hyperaccumulator Arabidopsis halleri. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5783-95. [PMID: 26044091 PMCID: PMC4566976 DOI: 10.1093/jxb/erv280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In Arabidopsis halleri, the HMA4 gene has an essential function in Zn/Cd hypertolerance and hyperaccumulation by mediating root-to-shoot translocation of metals. Constitutive high expression of AhHMA4 results from a tandem triplication and cis-activation of the promoter of all three copies. The three AhHMA4 copies possess divergent promoter sequences, but highly conserved coding sequences, and display identical expression profiles in the root and shoot vascular system. Here, an AhHMA4::GFP fusion was expressed under the control of each of the three A. halleri HMA4 promoters in a hma2hma4 double mutant of A. thaliana to individually examine the function of each AhHMA4 copy. The protein showed non-polar localization at the plasma membrane of the root pericycle cells of both A. thaliana and A. halleri. The expression of each AhHMA4::GFP copy complemented the severe Zn-deficiency phenotype of the hma2hma4 mutant by restoring root-to-shoot translocation of Zn. However, each copy had a different impact on metal homeostasis in the A. thaliana genetic background: AhHMA4 copies 2 and 3 were more highly expressed and provided higher Zn tolerance in roots and accumulation in shoots than copy 1, and AhHMA4 copy 3 also increased Cd tolerance in roots. These data suggest a certain extent of functional differentiation among the three A. halleri HMA4 copies, stemming from differences in expression levels rather than in expression profile. HMA4 is a key node of the Zn homeostasis network and small changes in expression level can have a major impact on Zn allocation to root or shoot tissues.
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Affiliation(s)
- Cécile Nouet
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Jean-Benoit Charlier
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Monique Carnol
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Bernard Bosman
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Frédéric Farnir
- Biostatistics and Bioinformatics, FARAH, Faculty of Veterinary Medicine, University of Liège, B-4000 Liège, Belgium
| | - Patrick Motte
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
| | - Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
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26
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Charlier JB, Polese C, Nouet C, Carnol M, Bosman B, Krämer U, Motte P, Hanikenne M. Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3865-78. [PMID: 25900619 PMCID: PMC4473987 DOI: 10.1093/jxb/erv188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In Arabidopsis thaliana, FRD3 (FERRIC CHELATE REDUCTASE DEFECTIVE 3) plays a central role in metal homeostasis. FRD3 is among a set of metal homeostasis genes that are constitutively highly expressed in roots and shoots of Arabidopsis halleri, a zinc hyperaccumulating and hypertolerant species. Here, we examined the regulation of FRD3 by zinc in both species to shed light on the evolutionary processes underlying the evolution of hyperaccumulation in A. halleri. We combined gene expression studies with the use of β-glucuronidase and green fluorescent protein reporter constructs to compare the expression profile and transcriptional and post-transcriptional regulation of FRD3 in both species. The AtFRD3 and AhFRD3 genes displayed a conserved expression profile. In A. thaliana, alternative transcription initiation sites from two promoters determined transcript variants that were differentially regulated by zinc supply in roots and shoots to favour the most highly translated variant under zinc-excess conditions. In A. halleri, a single transcript variant with higher transcript stability and enhanced translation has been maintained. The FRD3 gene thus undergoes complex transcriptional and post-transcriptional regulation in Arabidopsis relatives. Our study reveals that a diverse set of mechanisms underlie increased gene dosage in the A. halleri lineage and illustrates how an environmental challenge can alter gene regulation.
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Affiliation(s)
- Jean-Benoit Charlier
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Catherine Polese
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Cécile Nouet
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium
| | - Monique Carnol
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Bernard Bosman
- Laboratory of Plant and Microbial Ecology, Department of Biology, Ecology, Evolution, University of Liège, B-4000 Liège, Belgium
| | - Ute Krämer
- Department of Plant Physiology, Ruhr University Bochum, D-44801 Bochum, Germany
| | - Patrick Motte
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
| | - Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering (CIP), Department of Life Sciences, University of Liège, B-4000 Liège, Belgium PhytoSYSTEMS, University of Liège, B-4000 Liège, Belgium
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Hollister JD. Genomic variation in Arabidopsis: tools and insights from next-generation sequencing. Chromosome Res 2015; 22:103-15. [PMID: 24801344 DOI: 10.1007/s10577-014-9420-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The release of a reference genome for Arabidopsis thaliana in 2000 has been an enormous boon for the study of plant genetics. Less than a decade later, however, a revolution in sequencing technology had enabled rapid and inexpensive re-sequencing of whole A. thaliana genomes. Large-scale efforts to characterize natural genomic variation in A. thaliana have revealed remarkable intra-specific variation in this species, ranging from single-nucleotide differences to large structural rearrangements. The partitioning of this variation by geography and local adaptation has been described using powerful new methods and tools. Simultaneously, an ambitious research agenda has emerged to sequence 1001 A. thaliana lines from around the world, while sequencing of related species is enabling powerful evolutionary genomic analyses. In this review, I summarize recent progress in genomic analysis of natural variation in A. thaliana and its close relatives. This progress has set the stage for the emergence of Arabidopsis as a model genus for evolutionary and functional genomics.
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Affiliation(s)
- Jesse D Hollister
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 1G8, Canada,
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Wang X, Jin D, Wang Z, Guo H, Zhang L, Wang L, Li J, Paterson AH. Telomere-centric genome repatterning determines recurring chromosome number reductions during the evolution of eukaryotes. THE NEW PHYTOLOGIST 2015; 205:378-89. [PMID: 25138576 DOI: 10.1111/nph.12985] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/05/2014] [Indexed: 05/22/2023]
Abstract
Whole-genome duplication (WGD) is central to the evolution of many eukaryotic genomes, in particular rendering angiosperm (flowering plant) genomes much less stable than those of animals. Following repeated duplication/triplication(s), angiosperm chromosome numbers have usually been restored to a narrow range, as one element in a 'diploidization' process that re-establishes diploid heredity. In several angiosperms affected by WGD, we show that chromosome number reduction (CNR) is best explained by intra- and/or inter-chromosomal crossovers to form new chromosomes that utilize the existing telomeres of 'invaded' and centromeres of 'invading' chromosomes, the alternative centromeres and telomeres being lost. Comparison with the banana (Musa acuminata) genome supports a 'fusion model' for the evolution of rice (Oryza sativa) chromosomes 2 and 3, implying that the grass common ancestor had seven chromosomes rather than the five implied by a 'fission model.' The 'invading' and 'invaded' chromosomes are frequently homoeologs, originating from duplication of a common ancestral chromosome and with greater-than-average DNA-level correspondence to one another. Telomere-centric CNR following recursive WGD in plants is also important in mammals and yeast, and may be a general mechanism of restoring small linear chromosome numbers in higher eukaryotes.
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Affiliation(s)
- Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA; Center for Genomics and Computational Biology, Hebei United University, Tangshan, Hebei, 063000, China; College of Sciences, Hebei United University, Tangshan, Hebei, 063000, China; College of Life Sciences, Hebei United University, Tangshan, Hebei, 063000, China
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Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 2014; 10:e1004785. [PMID: 25393550 PMCID: PMC4230842 DOI: 10.1371/journal.pgen.1004785] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 09/26/2014] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is an ancient molecular modification found in most eukaryotes. In plants, DNA methylation is not only critical for transcriptionally silencing transposons, but can also affect phenotype by altering expression of protein coding genes. The extent of its contribution to phenotypic diversity over evolutionary time is, however, unclear, because of limited stability of epialleles that are not linked to DNA mutations. To dissect the relative contribution of DNA methylation to transposon surveillance and host gene regulation, we leveraged information from three species in the Brassicaceae that vary in genome architecture, Capsella rubella, Arabidopsis lyrata, and Arabidopsis thaliana. We found that the lineage-specific expansion and contraction of transposon and repeat sequences is the main driver of interspecific differences in DNA methylation. The most heavily methylated portions of the genome are thus not conserved at the sequence level. Outside of repeat-associated methylation, there is a surprising degree of conservation in methylation at single nucleotides located in gene bodies. Finally, dynamic DNA methylation is affected more by tissue type than by environmental differences in all species, but these responses are not conserved. The majority of DNA methylation variation between species resides in hypervariable genomic regions, and thus, in the context of macroevolution, is of limited phenotypic consequence. DNA methylation is an epigenetic mark that has received a great deal of attention in plants because it can be stably transmitted across generations. However, the rate of DNA methylation change, or epimutation, is greater than that of DNA mutation. In addition, different from DNA sequence, DNA methylation can vary within an individual in response to developmental or environmental cues. Whether altered characters can be passed on to the next generation via directed modifications in DNA methylation is a question of great interest. We have compared how DNA methylation changes between species, tissues, and environments using three closely related crucifers as examples. We found that DNA methylation is different between roots and shoots and changes with temperatures, but that such changes are not conserved across species. Moreover, most of the methylated sites are not conserved between species. This suggests that DNA methylation may respond to immediate fluctuations in the environment, but this response is not retained over long evolutionary periods. Thus, in contrast to transcriptional responses, conserved epigenetic responses at the level of DNA methylation are not widespread. Instead, the patterns of DNA methylation are largely determined by the evolution of genome structure, and responsive loci are likely short-lived accidents of this process.
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Rešetnik I, Frajman B, Bogdanović S, Ehrendorfer F, Schönswetter P. Disentangling relationships among the diploid members of the intricate genus Knautia (Caprifoliaceae, Dipsacoideae). Mol Phylogenet Evol 2014; 74:97-110. [PMID: 24508604 DOI: 10.1016/j.ympev.2014.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/19/2014] [Accepted: 01/27/2014] [Indexed: 01/05/2023]
Abstract
The genus Knautia (Caprifoliaceae, Dipsacoideae) encompasses 40-60 species mainly distributed in western Eurasia, with highest species diversity in the Alps and the Balkan Peninsula. It is traditionally regarded as one of the taxonomically most challenging European genera due to the widespread occurrence of polyploidy, the high incidence of hybridisation and the maintenance of morphologically intermediate forms. A prerequisite for assessing the complex spatiotemporal diversification of a polyploid group is a comprehensive hypothesis of the phylogenetic relationships among its diploid members. To this end, DNA sequence data (nrDNA ITS and plastid petN(ycf6)-psbM) combined with AFLP fingerprinting were performed on 148 diploid populations belonging to 35 taxa. Phylogenies obtained by maximum parsimony and Bayesian analyses were used to test the monophyly of the genus and its three sections Trichera, Tricheroides and Knautia, to provide insights into its evolutionary history and to test previous hypotheses of inter- and intrasectional classification. Both nuclear and chloroplast datasets support the monophyly of Knautia and its three sections, with ambiguous placement of K. cf. degenii. The majority of species belong to the nearly exclusively perennial section Trichera (x=10). Within section Trichera all markers revealed largely unresolved phylogenetic relationships suggesting rapid radiation and recent range expansion. In addition, extensive sharing of plastid haplotypes across taxa and wide geographic ranges of plastid haplotypes and ribotype groups were observed. The molecular data are partly at odds with the traditional informal grouping of taxa within section Trichera. Whereas the traditional groups of K. dinarica, K. drymeia and K. montana can be maintained, the new, smaller and well supported Midzorensis and Pancicii Groups as well as the SW European Group are separated from the heterogeneous traditional K. longifolia group. The former groups of K. arvensis, K. dalmatica, K. fleischmannii and K. velutina are clearly polyphyletic. Their diploid members have to be rearranged into the Xerophytic Group, the Carinthiaca Group, and the Northern and Southern Arvensis Groups. The annual sections Tricheroides (x=10) and Knautia (x=8) with only a few taxa are resolved in the ITS and plastid trees on long branches as early diverging lineages within the genus.
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Affiliation(s)
- Ivana Rešetnik
- Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10000 Zagreb, Croatia.
| | - Božo Frajman
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria.
| | - Sandro Bogdanović
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, HR-10000 Zagreb, Croatia.
| | - Friedrich Ehrendorfer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria.
| | - Peter Schönswetter
- Institute of Botany, University of Innsbruck, Sternwartestraße 15, A-6020 Innsbruck, Austria.
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He H, Liang G, Li Y, Wang F, Yu D. Two young MicroRNAs originating from target duplication mediate nitrogen starvation adaptation via regulation of glucosinolate synthesis in Arabidopsis thaliana. PLANT PHYSIOLOGY 2014; 164:853-65. [PMID: 24367020 PMCID: PMC3912111 DOI: 10.1104/pp.113.228635] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/22/2013] [Indexed: 05/18/2023]
Abstract
Nitrogen is an essential macronutrient required for plant growth and development. A number of genes respond to nitrogen starvation conditions. However, the functions of most of these nitrogen starvation-responsive genes are unclear. Our recent survey suggested that many microRNAs (miRNAs) are responsive to nitrogen starvation in Arabidopsis thaliana. Here, we identified a new miRNA (miR5090) from the complementary transcript of the MIR826 gene. Further investigation uncovered that both miRNA genes recently evolved from the inverse duplication of their common target gene, ALKENYL HYDROXALKYL PRODUCING2 (AOP2). Similar to miR826, miR5090 is induced by nitrogen starvation. By contrast, the AOP2 transcript level was negatively correlated with miR826 and miR5090 under nitrogen starvation. GUS-fused AOP2 expression suggested that AOP2 was posttranscriptionally suppressed by miR826 and miR5090. miRNA transgenic plants with significantly low AOP2 expression accumulated fewer Met-derived glucosinolates, phenocopying the aop2 mutants. Most glucosinolate synthesis-associated genes were repressed under nitrogen starvation conditions. Furthermore, miRNA transgenic plants with less glucosinolate displayed enhanced tolerance to nitrogen starvation, including high biomass, more lateral roots, increased chlorophyll, and decreased anthocyanin. Meanwhile, nitrogen starvation-responsive genes were up-regulated in transgenic plants, implying improved nitrogen uptake activity. Our study reveals a mechanism by which Arabidopsis thaliana regulates the synthesis of glucosinolates to adapt to environmental changes in nitrogen availability.
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MESH Headings
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Arabidopsis/drug effects
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis Proteins/genetics
- Base Sequence
- Chromatography, High Pressure Liquid
- Gene Duplication
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Genome, Plant/genetics
- Glucosinolates/biosynthesis
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Data
- Nitrogen/deficiency
- Nitrogen/pharmacology
- Phenotype
- Plants, Genetically Modified
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Homology, Nucleic Acid
- Transcription, Genetic/drug effects
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Genome-wide analysis of WRKY gene family in Arabidopsis lyrata and comparison with Arabidopsis thaliana and Populus trichocarpa. CHINESE SCIENCE BULLETIN-CHINESE 2014. [DOI: 10.1007/s11434-013-0057-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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33
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Coman D, Altenhoff A, Zoller S, Gruissem W, Vranová E. Distinct evolutionary strategies in the GGPPS family from plants. FRONTIERS IN PLANT SCIENCE 2014; 5:230. [PMID: 24904625 PMCID: PMC4034038 DOI: 10.3389/fpls.2014.00230] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/09/2014] [Indexed: 05/07/2023]
Abstract
Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate (GGPP) exist in plants. GGPP is produced in the isoprenoid pathway and is a central precursor for various primary and specialized plant metabolites. Therefore, its biosynthesis is an essential regulatory point in the isoprenoid pathway. We selected 119 GGPPSs from 48 species representing all major plant lineages, based on stringent homology criteria. After the diversification of land plants, the number of GGPPS paralogs per species increases. Already in the moss Physcomitrella patens, GGPPS appears to be encoded by multiple paralogous genes. In gymnosperms, neofunctionalization of GGPPS may have enabled optimized biosynthesis of primary and specialized metabolites. Notably, lineage-specific expansion of GGPPS occurred in land plants. As a representative species we focused here on Arabidopsis thaliana, which retained the highest number of GGPPS paralogs (twelve) among the 48 species we considered in this study. Our results show that the A. thaliana GGPPS gene family is an example of evolution involving neo- and subfunctionalization as well as pseudogenization. We propose subfunctionalization as one of the main mechanisms allowing the maintenance of multiple GGPPS paralogs in A. thaliana genome. Accordingly, the changes in the expression patterns of the GGPPS paralogs occurring after gene duplication led to developmental and/or condition specific functional evolution.
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Affiliation(s)
- Diana Coman
- Department of Biology, ETH ZurichZurich, Switzerland
| | - Adrian Altenhoff
- Department of Computer Science, ETH ZurichZurich, Switzerland
- Swiss Institute of BioinformaticsZurich, Switzerland
| | - Stefan Zoller
- Department of Computer Science, ETH ZurichZurich, Switzerland
- Swiss Institute of BioinformaticsZurich, Switzerland
| | | | - Eva Vranová
- Department of Biology, ETH ZurichZurich, Switzerland
- Institute of Biology and Ecology, Pavol Jozef Šafárik UniversityKošice, Slovakia
- *Correspondence: Eva Vranová, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Šafárik University in Košice, Mánesova 23, Košice, 04154, Slovakia e-mail:
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Yang L, Koo DH, Li D, Zhang T, Jiang J, Luan F, Renner SS, Hénaff E, Sanseverino W, Garcia-Mas J, Casacuberta J, Senalik DA, Simon PW, Chen J, Weng Y. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:16-30. [PMID: 24127692 DOI: 10.1111/tpj.12355] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 10/07/2013] [Accepted: 10/10/2013] [Indexed: 05/22/2023]
Abstract
In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
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Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. BIOLOGY 2013; 2:1465-87. [PMID: 24833233 PMCID: PMC4009786 DOI: 10.3390/biology2041465] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 12/17/2022]
Abstract
Arabidopsis thaliana became the model organism for plant studies because of its small diploid genome, rapid lifecycle and short adult size. Its genome was the first among plants to be sequenced, becoming the reference in plant genomics. However, the Arabidopsis genome is characterized by an inherently complex organization, since it has undergone ancient whole genome duplications, followed by gene reduction, diploidization events and extended rearrangements, which relocated and split up the retained portions. These events, together with probable chromosome reductions, dramatically increased the genome complexity, limiting its role as a reference. The identification of paralogs and single copy genes within a highly duplicated genome is a prerequisite to understand its organization and evolution and to improve its exploitation in comparative genomics. This is still controversial, even in the widely studied Arabidopsis genome. This is also due to the lack of a reference bioinformatics pipeline that could exhaustively identify paralogs and singleton genes. We describe here a complete computational strategy to detect both duplicated and single copy genes in a genome, discussing all the methodological issues that may strongly affect the results, their quality and their reliability. This approach was used to analyze the organization of Arabidopsis nuclear protein coding genes, and besides classifying computationally defined paralogs into networks and single copy genes into different classes, it unraveled further intriguing aspects concerning the genome annotation and the gene relationships in this reference plant species. Since our results may be useful for comparative genomics and genome functional analyses, we organized a dedicated web interface to make them accessible to the scientific community
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Fletcher RS, Mullen JL, Yoder S, Bauerle WL, Reuning G, Sen S, Meyer E, Juenger TE, McKay JK. Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits. BMC Genomics 2013; 14:655. [PMID: 24063355 PMCID: PMC3849958 DOI: 10.1186/1471-2164-14-655] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/20/2013] [Indexed: 12/30/2022] Open
Abstract
Background The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.
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Affiliation(s)
- Richard S Fletcher
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 80523 Fort Collins, CO, USA.
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Liu Z, Lv Y, Zhang M, Liu Y, Kong L, Zou M, Lu G, Cao J, Yu X. Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis). BMC Genomics 2013; 14:594. [PMID: 24001366 PMCID: PMC3766048 DOI: 10.1186/1471-2164-14-594] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/22/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families. RESULTS In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated. CONCLUSIONS The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous hormones, such as 6-BA and ABA, suggesting their potential roles in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. The appropriate modulation of endogenous CKs levels by IPT and CKX genes is a promising approach for developing economically important high-yielding and high-quality stress-tolerant crops in agriculture.
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Affiliation(s)
- Zhenning Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P,R,China.
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Truco MJ, Ashrafi H, Kozik A, van Leeuwen H, Bowers J, Wo SRC, Stoffel K, Xu H, Hill T, Van Deynze A, Michelmore RW. An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce. G3 (BETHESDA, MD.) 2013; 3:617-631. [PMID: 23550116 PMCID: PMC3618349 DOI: 10.1534/g3.112.004929] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/07/2013] [Indexed: 02/07/2023]
Abstract
We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.
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Affiliation(s)
- Maria José Truco
- The Genome Center, University of California, Davis, California 95616
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Alexander Kozik
- The Genome Center, University of California, Davis, California 95616
| | - Hans van Leeuwen
- The Genome Center, University of California, Davis, California 95616
| | - John Bowers
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | | | - Kevin Stoffel
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Huaqin Xu
- The Genome Center, University of California, Davis, California 95616
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, California 95616
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, California 95616
- Department of Plant Sciences, University of California, Davis, California 95616
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Charon C, Bruggeman Q, Thareau V, Henry Y. Gene duplication within the Green Lineage: the case of TEL genes. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:5061-5077. [PMID: 22865910 DOI: 10.1093/jxb/ers181] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent years have witnessed a breathtaking increase in the availability of genome sequence data, providing evidence of the highly duplicate nature of eukaryotic genomes. Plants are exceptional among eukaryotic organisms in that duplicate loci compose a large fraction of their genomes, partly because of the frequent occurrence of polyploidy (or whole-genome duplication) events. Tandem gene duplication and transposition have also contributed to the large number of duplicated genes in plant genomes. Evolutionary analyses allowed the dynamics of duplicate gene evolution to be studied and several models were proposed. It seems that, over time, many duplicated genes were lost and some of those that were retained gained new functions and/or expression patterns (neofunctionalization) or subdivided their functions and/or expression patterns between them (subfunctionalization). Recent studies have provided examples of genes that originated by duplication with successive diversification within plants. In this review, we focused on the TEL (TERMINAL EAR1-like) genes to illustrate such mechanisms. Emerged from the mei2 gene family, these TEL genes are likely to be land plant-specific. Phylogenetic analyses revealed one or two TEL copies per diploid genome. TEL gene degeneration and loss in several Angiosperm species such as in poplar and maize seem to have occurred. In Arabidopsis thaliana, whose genome experienced at least three polyploidy events followed by massive gene loss and genomic reorganization, two TEL genes were retained and two new shorter TEL-like (MCT) genes emerged. Molecular and expression analyses suggest for these genes sub- and neofunctionalization events, but confirmation will come from their functional characterization.
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Affiliation(s)
- Céline Charon
- Institut de Biologie des Plantes-CNRS (UMR8618), Université Paris-Sud 11, Saclay Plant Sciences, F-91405 Orsay Cedex, France.
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Alcázar R, Pecinka A, Aarts MGM, Fransz PF, Koornneef M. Signals of speciation within Arabidopsis thaliana in comparison with its relatives. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:205-211. [PMID: 22265228 DOI: 10.1016/j.pbi.2012.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/06/2011] [Accepted: 01/03/2012] [Indexed: 05/31/2023]
Abstract
The species within the now well-defined Arabidopsis genus provide biological materials suitable to investigate speciation and the development of reproductive isolation barriers between related species. Even within the model species A. thaliana, genetic differentiation between populations due to environmental adaptation or demographic history can lead to cases where hybrids between accessions are non-viable. Experimental evidence supports the importance of genome duplications and genetic epistatic interactions in the occurrence of reproductive isolation. Other examples of adaptation to specific environments can be found in Arabidopsis relatives where hybridization and chromosome doubling lead to new amphidiploid species. Molecular signals of speciation found in the Arabidopsis genus should provide a better understanding of speciation processes in plants from a genetic, molecular and evolutionary perspective.
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Affiliation(s)
- Rubén Alcázar
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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Irwin JA, Lister C, Soumpourou E, Zhang Y, Howell EC, Teakle G, Dean C. Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome. BMC PLANT BIOLOGY 2012; 12:21. [PMID: 22333192 PMCID: PMC3299615 DOI: 10.1186/1471-2229-12-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/14/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea. RESULTS We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana. CONCLUSIONS We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is not syntenic with A. thaliana FRI due to an ancient recombination event. This has complicated previous association analyses of FRI with variation in life history strategy in the Brassica genus.
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Affiliation(s)
- Judith A Irwin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Clare Lister
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eleni Soumpourou
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yanwen Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Elaine C Howell
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Wellesbourne CV35 9EF, UK
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Feraru E, Vosolsobě S, Feraru MI, Petrášek J, Kleine-Vehn J. Evolution and Structural Diversification of PILS Putative Auxin Carriers in Plants. FRONTIERS IN PLANT SCIENCE 2012; 3:227. [PMID: 23091477 PMCID: PMC3470039 DOI: 10.3389/fpls.2012.00227] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 09/21/2012] [Indexed: 05/21/2023]
Abstract
The phytohormone auxin contributes to virtually every aspect of the plant development. The spatiotemporal distribution of auxin depends on a complex interplay between auxin metabolism and intercellular auxin transport. Intracellular auxin compartmentalization provides another link between auxin transport processes and auxin metabolism. The PIN-LIKES (PILS) putative auxin carriers localize to the endoplasmic reticulum (ER) and contribute to cellular auxin homeostasis. PILS proteins regulate intracellular auxin accumulation, the rate of auxin conjugation and, subsequently, affect nuclear auxin signaling. Here, we investigate sequence diversification of the PILS family in Arabidopsis thaliana and provide insights into the evolution of these novel putative auxin carriers in plants. Our data suggest that PILS proteins are conserved throughout the plant lineage and expanded during higher plant evolution. PILS proteins diversified early during plant evolution into three clades. Besides the ancient Clade I encompassing non-land plant species, PILS proteins evolved into two clades. The diversification of Clade II and Clade III occurred already at the level of non-vascular plant evolution and, hence, both clades contain vascular and non-vascular plant species. Nevertheless, Clade III contains fewer non- and increased numbers of vascular plants, indicating higher importance of Clade III for vascular plant evolution. Notably, PILS proteins are distinct and appear evolutionarily older than the prominent PIN-FORMED auxin carriers. Moreover, we revealed particular PILS sequence divergence in Arabidopsis and assume that these alterations could contribute to distinct gene regulations and protein functions.
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Affiliation(s)
- Elena Feraru
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life SciencesVienna, Austria
| | - Stanislav Vosolsobě
- Department of Faculty of Science, Experimental Plant Biology, Charles UniversityPrague, Czech Republic
| | - Mugurel I. Feraru
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life SciencesVienna, Austria
| | - Jan Petrášek
- Department of Faculty of Science, Experimental Plant Biology, Charles UniversityPrague, Czech Republic
- Institute of Experimental Botany of the Academy of Sciences of the Czech RepublicPrague, Czech Republic
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life SciencesVienna, Austria
- *Correspondence: Jürgen Kleine-Vehn, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria. e-mail:
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Bliss BJ, Suzuki JY. Genome size in Anthurium evaluated in the context of karyotypes and phenotypes. AOB PLANTS 2012; 2012:pls006. [PMID: 22509462 PMCID: PMC3326669 DOI: 10.1093/aobpla/pls006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 02/17/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Anthurium is an important horticultural crop from the family Araceae, order Alismatales, a lineage considered to have diverged from other monocots prior to the cereals. Genome size and its distribution in Anthurium were investigated to gain a basic understanding of genome organization in this large genus and to forge a firm foundation for advancement of molecular approaches for the study of Anthurium. Currently, genome size estimates have been reported for only two Anthurium samples. METHODOLOGY Bulk nuclear DNA content estimates were obtained by flow cell cytometry using leaf tissue collected from Anthurium species of different subgeneric groups and from commercial cultivars. The most current and well-supported topology of subgeneric, sectional relationships was applied to present genome size estimates in the context of reported chromosome counts, karyotypes, putative phylogenetic relationships, observed phenotypes and pedigree. PRINCIPAL RESULTS Genome size estimates based on bulk nuclear DNA content for 77 accessions representing 34 species and 9 cultivars were obtained, including initial estimates for 33 Anthurium species, and both the smallest (Anthurium obtusum; Tetraspermium) and largest (Anthurium roseospadix; Calomystrium) Anthurium genome sizes reported to date. Genome size did not distinguish any subgeneric section, but ranged 5-fold (4.42-20.83 pg/2 C) despite consistent 2N= 30 chromosome counts. Intraspecies genome size variation >20 % is reported for Anthurium ravenii, A. watermaliense and A. gracile. CONCLUSIONS Genome size estimates for Anthurium species spanning 13 recognized subgeneric sections indicate that genome size does not generally correlate with chromosome count or phylogenetic relationships. Mechanisms of genome expansion and contraction, including amplification and reduction of repetitive elements, polyploidy, chromosome reorganization/loss, may be involved in genome evolution in Anthurium as in other species. The new information on Anthurium genome sizes provides a platform for molecular studies supporting further research on genome evolution as well as cultivar development.
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Ng DWK, Zhang C, Miller M, Shen Z, Briggs SP, Chen ZJ. Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity (Edinb) 2011; 108:419-30. [PMID: 22009271 DOI: 10.1038/hdy.2011.92] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Autopolyploidy and allopolyploidy are common in many plants and some animals. Rapid changes in genomic composition and gene expression have been observed in both autopolyploids and allopolyploids, but the effects of polyploidy on proteomic divergence are poorly understood. Here, we report quantitative analysis of protein changes in leaves of Arabidopsis autopolyploids and allotetraploids and their progenitors using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with mass spectrometry. In more than 1000 proteins analyzed, the levels of protein divergence were relatively high (~18%) between Arabidopsis thaliana and Arabidopsis arenosa, relatively low (~6.8%) between an A. thaliana diploid and autotetraploid and intermediate (~8.3 and 8.2%) in F(1)- and F(8)-resynthesized allotetraploids relative to mid-parent values, respectively. This pattern of proteomic divergence was consistent with the previously reported gene expression data. In particular, many non-additively accumulated proteins (61-62%) in the F(1) and F(8) allotetraploids were also differentially expressed between the parents. The differentially accumulated proteins in functional categories of abiotic and biotic stresses were overrepresented between an A. thaliana autotetraploid and diploid and between two Arabidopsis species, but not significantly different between allotetraploids and their progenitors. Although the trend of changes is similar, the percentage of differentially accumulated proteins that matched previously reported differentially expressed genes was relatively low. Western blot analysis confirmed several selected proteins with isoforms the cumulative levels of which were differentially expressed. These data suggest high protein divergence between species and rapid changes in post-transcriptional regulation and translational modifications of proteins during polyploidization.
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Affiliation(s)
- D W-K Ng
- Section of Molecular Cell and Developmental Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX, USA
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Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011; 43:1035-9. [PMID: 21873998 DOI: 10.1038/ng.919] [Citation(s) in RCA: 1281] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/03/2011] [Indexed: 11/09/2022]
Abstract
We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.
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Affiliation(s)
- Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (IVF, CAAS), Beijing, China
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Li F, Hasegawa Y, Saito M, Shirasawa S, Fukushima A, Ito T, Fujii H, Kishitani S, Kitashiba H, Nishio T. Extensive chromosome homoeology among Brassiceae species were revealed by comparative genetic mapping with high-density EST-based SNP markers in radish (Raphanus sativus L.). DNA Res 2011; 18:401-11. [PMID: 21816873 PMCID: PMC3190960 DOI: 10.1093/dnares/dsr027] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another.
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Affiliation(s)
- Feng Li
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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47
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Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Pląder W, Seroczyńska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpiński S, Malepszy S, Przybecki Z. The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants. PLoS One 2011; 6:e22728. [PMID: 21829493 PMCID: PMC3145757 DOI: 10.1371/journal.pone.0022728] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Accepted: 07/05/2011] [Indexed: 01/01/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.
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MESH Headings
- Adaptation, Physiological
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/genetics
- Cucumis sativus/genetics
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Genome, Plant
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Regulatory Sequences, Nucleic Acid
- Sequence Analysis, DNA
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Affiliation(s)
- Rafał Wóycicki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Justyna Witkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Joanna Dąbrowska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Alexandre Lomsadze
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Kohei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Anna Seroczyńska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Mieczysław Śmiech
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Wojciech Gutman
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University, Higashi-ku, Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, Tokai University, Minamiaso-mura, Kumamoto, Japan
| | - Mark Borodovsky
- Center for Bioinformatics and Computational Genomics, Joint Wallace H. Coulter Georgia Tech and Emory Department of Biomedical Engineering, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stanisław Karpiński
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw University of Life Sciences - SGGW, Nowoursynowska, Warsaw, Poland
- * E-mail: (ZP); (SK); (RW)
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48
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Hanikenne M, Nouet C. Metal hyperaccumulation and hypertolerance: a model for plant evolutionary genomics. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:252-9. [PMID: 21531166 DOI: 10.1016/j.pbi.2011.04.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 04/04/2011] [Accepted: 04/07/2011] [Indexed: 05/21/2023]
Abstract
In the course of evolution, plants adapted to widely differing metal availabilities in soils and therefore represent an important source of natural variation of metal homeostasis networks. Research on plant metal homeostasis can thus provide insights into the functioning, regulation and adaptation of biological networks. Here, we describe major recent breakthroughs in the understanding of the genetic and molecular basis of metal hyperaccumulation and associated hypertolerance, a naturally selected complex trait which represents an extreme adaptation of the metal homeostasis network. Investigations in this field reveal further the molecular alterations underlying the evolution of natural phenotypic diversity and provide a highly relevant framework for comparative genomics.
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Affiliation(s)
- Marc Hanikenne
- Functional Genomics and Plant Molecular Imaging, Center for Protein Engineering, Department of Life Sciences (B22), University of Liège, Liège, Belgium.
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Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics 2011; 12:102. [PMID: 21501495 PMCID: PMC3088904 DOI: 10.1186/1471-2105-12-102] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 04/18/2011] [Indexed: 12/01/2022] Open
Abstract
Background It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. Results We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons). Conclusions The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl, offering easier access to thousands of genomes for non-programmers.
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Affiliation(s)
- Haibao Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
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50
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Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KFX, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet 2011; 43:476-81. [PMID: 21478890 PMCID: PMC3083492 DOI: 10.1038/ng.807] [Citation(s) in RCA: 596] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 03/18/2011] [Indexed: 12/19/2022]
Abstract
We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.
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Affiliation(s)
- Tina T Hu
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
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