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Ireland HS, Wu C, Deng CH, Hilario E, Saei A, Erasmuson S, Crowhurst RN, David KM, Schaffer RJ, Chagné D. The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae. Hortic Res 2021; 8:233. [PMID: 34719690 PMCID: PMC8558331 DOI: 10.1038/s41438-021-00662-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/28/2021] [Accepted: 07/30/2021] [Indexed: 05/03/2023]
Abstract
The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a 'rosetta stone' for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.
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Affiliation(s)
- Hilary S Ireland
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Ali Saei
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Sylvia Erasmuson
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 4704, Christchurch Mail Centre, Christchurch, 8140, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 92196, Auckland Mail Centre, Auckland, 1142, New Zealand
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Karine M David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
| | - Robert J Schaffer
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland, 1142, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, 55 Old Mill Road, RD 3, Motueka, 7198, New Zealand
| | - David Chagné
- Genomics Aotearoa, ℅ Department of Biochemistry, University of Otago, PO Box 56, Dunedin, 9054, New Zealand.
- The New Zealand Institute for Plant and Food Research Ltd, Private Bag 11600, Palmerston North, 4442, New Zealand.
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Popowski E, Thomson SJ, Knäbel M, Tahir J, Crowhurst RN, Davy M, Foster TM, Schaffer RJ, Tustin DS, Allan AC, McCallum J, Chagné D. Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing. G3 (Bethesda) 2021; 11:6261761. [PMID: 34009255 PMCID: PMC8495948 DOI: 10.1093/g3journal/jkab142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/07/2021] [Indexed: 11/19/2022]
Abstract
Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed Actinidia chinensis var. chinensis, is either diploid (2n = 2x = 58) or tetraploid (2n = 4x = 116) and the green-fleshed cultivar A. chinensis var. deliciosa “Hayward,” is hexaploid (2n = 6x = 174). Advances in breeding green kiwifruit could be greatly sped up by the use of molecular resources for more efficient and faster selection, for example using marker-assisted selection (MAS). The key genetic marker that has been implemented for MAS in hexaploid kiwifruit is for gender testing. The limited marker-trait association has been reported for other polyploid kiwifruit for fruit and production traits. We have constructed a high-density linkage map for hexaploid green kiwifruit using genotyping-by-sequence (GBS). The linkage map obtained consists of 3686 and 3940 markers organized in 183 and 176 linkage groups for the female and male parents, respectively. Both parental linkage maps are co-linear with the A. chinensis “Red5” reference genome of kiwifruit. The linkage map was then used for quantitative trait locus (QTL) mapping, and successfully identified QTLs for king flower number, fruit number and weight, dry matter accumulation, and storage firmness. These are the first QTLs to be reported and discovered for complex traits in hexaploid kiwifruit.
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Affiliation(s)
- Elizabeth Popowski
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | | | | | | | - Marcus Davy
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Te Puke, New Zealand
| | | | - Robert J Schaffer
- Plant & Food Research, Motueka, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - Andrew C Allan
- Plant & Food Research, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | | | - David Chagné
- Plant & Food Research, Palmerston North, New Zealand
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Lang C, Karunairetnam S, Lo KR, Kralicek AV, Crowhurst RN, Gleave AP, MacDiarmid RM, Ingram JR. Common Variants of the Plant microRNA-168a Exhibit Differing Silencing Efficacy for Human Low-Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1). Microrna 2019; 8:166-170. [PMID: 30501607 DOI: 10.2174/2211536608666181203103233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/25/2018] [Accepted: 11/26/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The discovery that a plant microRNA (miRNAs) from rice (Oryza sativa miR168a) can modify post-transcriptional expression of the mammalian. Low-Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) gene highlights the potential for cross-kingdom miRNAmRNA interactions. OBJECTIVE To investigate whether common variants of the conserved miR168a family have the capability for similar cross-kingdom regulatory functions, we selected sequences from three dietary plant sources: rice (Oryza sativa), tomato (Solanum lycopersicum), apple (Malus domestica) and compared their ability to regulate human LDLRAP1 expression. METHODS Target prediction software intaRNA and RNAhybrid were used to analyze and calculate the energy and alignment score between the miR168a variants and human LDLRAP1 mRNA. An in vitro cell-based Dual-Luciferase® Reporter Assay (pmirGLO, Promega), was then used to validate the miRNA-mRNA interaction experimentally. RESULTS Computational analyses revealed that a single nucleotide difference at position 14 (from the 5' end of the miRNA) creates a G:U wobble in the miRNA-mRNA duplex formed by tomato and apple miR168a variants. This G:U wobble had only a small effect on the free energy score (-33.8-34.7 kcal/mol). However, despite reasonable hybridization energy scores (<-20 kcal/mol) for all miR168a variants, only the rice miR168a variant lacking a G:U wobble significantly reduced LDLRAP1 transcript expression by 25.8 + 7.3% (p<0.05), as measured by relative luciferase activity. CONCLUSION In summary, single nucleotide differences at key positions can have a marked influence on regulatory function despite similar predicted energy scores and miRNA-mRNA duplex structures.
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Affiliation(s)
- Claudia Lang
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | | | - Kim R Lo
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | - Andrew V Kralicek
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | - Andrew Peter Gleave
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | - Robin M MacDiarmid
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
| | - John Ronald Ingram
- The New Zealand Institute for Plant & Food Research Ltd., Auckland 1142, New Zealand
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Wu C, Twort VG, Crowhurst RN, Newcomb RD, Buckley TR. Assembling large genomes: analysis of the stick insect (Clitarchus hookeri) genome reveals a high repeat content and sex-biased genes associated with reproduction. BMC Genomics 2017; 18:884. [PMID: 29145825 PMCID: PMC5691397 DOI: 10.1186/s12864-017-4245-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/31/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south. Here, we present a de novo genome assembly of a female C. hookeri and use it to detect candidate genes associated with gamete production and development in females and males. We also explore the factors underlying large genome size in stick insects. RESULTS The C. hookeri genome assembly was 4.2 Gb, similar to the flow cytometry estimate, making it the second largest insect genome sequenced and assembled to date. Like the large genome of Locusta migratoria, the genome of C. hookeri is also highly repetitive and the predicted gene models are much longer than those from most other sequenced insect genomes, largely due to longer introns. Miniature inverted repeat transposable elements (MITEs), absent in the much smaller T. cristinae genome, is the most abundant repeat type in the C. hookeri genome assembly. Mapping RNA-Seq reads from female and male gonadal transcriptomes onto the genome assembly resulted in the identification of 39,940 gene loci, 15.8% and 37.6% of which showed female-biased and male-biased expression, respectively. The genes that were over-expressed in females were mostly associated with molecular transportation, developmental process, oocyte growth and reproductive process; whereas, the male-biased genes were enriched in rhythmic process, molecular transducer activity and synapse. Several genes involved in the juvenile hormone synthesis pathway were also identified. CONCLUSIONS The evolution of large insect genomes such as L. migratoria and C. hookeri genomes is most likely due to the accumulation of repetitive regions and intron elongation. MITEs contributed significantly to the growth of C. hookeri genome size yet are surprisingly absent from the T. cristinae genome. Sex-biased genes identified from gonadal tissues, including genes involved in juvenile hormone synthesis, provide interesting candidates for the further study of flexible reproduction in stick insects.
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Affiliation(s)
- Chen Wu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- Department of Biology, Lund University, Lund, Sweden
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
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Wu C, Jordan MD, Newcomb RD, Gemmell NJ, Bank S, Meusemann K, Dearden PK, Duncan EJ, Grosser S, Rutherford K, Gardner PP, Crowhurst RN, Steinwender B, Tooman LK, Stevens MI, Buckley TR. Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution. BMC Genomics 2017; 18:795. [PMID: 29041914 PMCID: PMC5644144 DOI: 10.1186/s12864-017-4197-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/08/2017] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. RESULTS Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×. DNA elements, LTRs and simple repeats and LINEs formed the largest components and SINEs were very rare. Phylogenomics (370,877 amino acids) placed H. duospinosa within the Neanuridae. We recovered orthologs of the conserved sex determination genes thought to play a role in sex determination. Analysis of CpG content suggested the absence of DNA methylation, and consistent with this we were unable to detect orthologs of the DNA methyltransferase enzymes. The small subunit rRNA gene contained a possible retrotransposon. The Hox gene complex was broken over two scaffolds. For chemosensory ability, at least 15 and 18 ionotropic glutamate and gustatory receptors were identified, respectively. However, we were unable to identify any odorant receptors or their obligate co-receptor Orco. Twenty-three chitinase-like genes were identified from the assembly. Members of this multigene family may play roles in the digestion of fungal cell walls, a common food source for these saproxylic organisms. We also detected 59 and 96 genes that blasted to bacteria and fungi, respectively, but were located on scaffolds that otherwise contained arthropod genes. CONCLUSIONS The genome of H. duospinosa contains some unusual features including a Hox complex broken over two scaffolds, in a different manner to other arthropod species, a lack of odorant receptor genes and an apparent lack of environmentally responsive DNA methylation, unlike many other arthropods. Our detection of candidate horizontal gene transfer candidates confirms that this phenomenon is occurring across Collembola. These findings allow us to narrow down the regions of the arthropod phylogeny where key innovations have occurred that have facilitated the evolutionary success of Hexapoda.
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Affiliation(s)
- Chen Wu
- Landcare Research, Private Bag, Auckland, 92170, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa D Jordan
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Sarah Bank
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Freiburg, Germany
| | - Peter K Dearden
- Genetics Otago, Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sefanie Grosser
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-, Martinsried, Germany
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ross N Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Bernd Steinwender
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Leah K Tooman
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, GPO Box 234, Adelaide, SA, 5001, Australia
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia
| | - Thomas R Buckley
- Landcare Research, Private Bag, Auckland, 92170, New Zealand.
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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Schwinn KE, Ngo H, Kenel F, Brummell DA, Albert NW, McCallum JA, Pither-Joyce M, Crowhurst RN, Eady C, Davies KM. The Onion ( Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis. Front Plant Sci 2016; 7:1865. [PMID: 28018399 PMCID: PMC5146992 DOI: 10.3389/fpls.2016.01865] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/25/2016] [Indexed: 05/18/2023]
Abstract
Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species.
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Affiliation(s)
- Kathy E. Schwinn
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Hanh Ngo
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Fernand Kenel
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - David A. Brummell
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - Nick W. Albert
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
| | - John A. McCallum
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Meeghan Pither-Joyce
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Ross N. Crowhurst
- The New Zealand Institute for Plant & Food Research LimitedAuckland, New Zealand
| | - Colin Eady
- The New Zealand Institute for Plant & Food Research LimitedChristchurch, New Zealand
| | - Kevin M. Davies
- The New Zealand Institute for Plant & Food Research LimitedPalmerston North, New Zealand
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Wu C, Crowhurst RN, Dennis AB, Twort VG, Liu S, Newcomb RD, Ross HA, Buckley TR. De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction. PLoS One 2016; 11:e0157783. [PMID: 27336743 PMCID: PMC4919086 DOI: 10.1371/journal.pone.0157783] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/03/2016] [Indexed: 11/21/2022] Open
Abstract
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
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Affiliation(s)
- Chen Wu
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Alice B. Dennis
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Victoria G. Twort
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Shen Zhen, China
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Howard A. Ross
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R. Buckley
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Bally J, Nakasugi K, Jia F, Jung H, Ho SYW, Wong M, Paul CM, Naim F, Wood CC, Crowhurst RN, Hellens RP, Dale JL, Waterhouse PM. The extremophile Nicotiana benthamiana has traded viral defence for early vigour. Nat Plants 2015; 1:15165. [PMID: 27251536 DOI: 10.1038/nplants.2015.165] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/01/2015] [Indexed: 05/03/2023]
Abstract
A single lineage of Nicotiana benthamiana is widely used as a model plant(1) and has been instrumental in making revolutionary discoveries about RNA interference (RNAi), viral defence and vaccine production. It is peerless in its susceptibility to viruses and its amenability in transiently expressing transgenes(2,3). These unparalleled characteristics have been associated both positively and negatively with a disruptive insertion in the RNA-dependent RNA polymerase 1 gene, Rdr1(4-6). For a plant so routinely used in research, the origin, diversity and evolution of the species, and the basis of its unusual abilities, have been relatively unexplored. Here, by comparison with wild accessions from across the spectrum of the species' natural distribution, we show that the laboratory strain of N. benthamiana is an extremophile originating from a population that has retained a mutation in Rdr1 for ∼0.8 Myr and thereby traded its defence capacity for early vigour and survival in the extreme habitat of central Australia. Reconstituting Rdr1 activity in this isolate provided protection. Silencing the functional allele in a wild strain rendered it hypersusceptible and was associated with a doubling of seed size and enhanced early growth rate. These findings open the way to a deeper understanding of the delicate balance between protection and vigour.
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Affiliation(s)
- Julia Bally
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Kenlee Nakasugi
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fangzhi Jia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Simon Y W Ho
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mei Wong
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chloe M Paul
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Fatima Naim
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Craig C Wood
- Commonwealth Scientific and Industrial Research Organisation-Plant Industry, Canberra, Australia
| | - Ross N Crowhurst
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - James L Dale
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
- School of Molecular Biology, The University of Sydney, Sydney, New South Wales 2006, Australia
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
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Thompson SM, Johnson CP, Lu AY, Frampton RA, Sullivan KL, Fiers MWEJ, Crowhurst RN, Pitman AR, Scott IAW, Wen A, Gudmestad NC, Smith GR. Genomes of 'Candidatus Liberibacter solanacearum' Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species. Phytopathology 2015; 105:863-871. [PMID: 25822188 DOI: 10.1094/phyto-12-14-0363-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
'Candidatus Liberibacter solanacearum' contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of 'Ca. L. solanacearum'-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A-B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.
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Affiliation(s)
- Sarah M Thompson
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Chris P Johnson
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ashley Y Lu
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Rebekah A Frampton
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Kerry L Sullivan
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Mark W E J Fiers
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ross N Crowhurst
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Andrew R Pitman
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Ian A W Scott
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Aimin Wen
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Neil C Gudmestad
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
| | - Grant R Smith
- First, third, fourth, fifth, sixth, eighth, ninth, and twelfth authors: The New Zealand Institute for Plant & Food Research Limited, Lincoln 7608, New Zealand; first, third, fourth, fifth, eighth, ninth, and twelfth authors: Plant Biosecurity Cooperative Research Centre, Canberra, ACT 2617, Australia; second, tenth, and eleventh authors: Department of Plant Pathology, North Dakota State University, Fargo 58108; and seventh author: The New Zealand Institute for Plant & Food Research Limited, Mt Albert 1025, New Zealand
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Corcoran JA, Jordan MD, Thrimawithana AH, Crowhurst RN, Newcomb RD. The Peripheral Olfactory Repertoire of the Lightbrown Apple Moth, Epiphyas postvittana. PLoS One 2015; 10:e0128596. [PMID: 26017144 PMCID: PMC4446339 DOI: 10.1371/journal.pone.0128596] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/28/2015] [Indexed: 01/10/2023] Open
Abstract
The lightbrown apple moth, Epiphyas postvittana is an increasingly global pest of horticultural crops. Like other moths, E. postvittana relies on olfactory cues to locate mates and oviposition sites. To detect these cues, moths have evolved families of genes encoding elements of the peripheral olfactory reception system, including odor carriers, receptors and degrading enzymes. Here we undertake a transcriptomic approach to identify members of these families expressed in the adult antennae of E. postvittana, describing open reading frames encoding 34 odorant binding proteins, 13 chemosensory proteins, 70 odorant receptors, 19 ionotropic receptors, nine gustatory receptors, two sensory neuron membrane proteins, 27 carboxylesterases, 20 glutathione-S-transferases, 49 cytochrome p450s and 18 takeout proteins. For the odorant receptors, quantitative RT-PCR corroborated RNAseq count data on steady state transcript levels. Of the eight odorant receptors that group phylogenetically with pheromone receptors from other moths, two displayed significant male-biased expression patterns, one displayed significant female-biased expression pattern and five were expressed equally in the antennae of both sexes. In addition, we found two male-biased odorant receptors that did not group with previously described pheromone receptors. This suite of olfaction-related genes provides a substantial resource for the functional characterization of this signal transduction system and the development of odor-mediated control strategies for horticultural pests.
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Affiliation(s)
- Jacob A. Corcoran
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Melissa D. Jordan
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | | | - Ross N. Crowhurst
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Richard D. Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
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11
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Chagné D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P, Bianco L, Lu A, Storey R, Knäbel M, Saeed M, Montanari S, Kim YK, Nicolini D, Larger S, Stefani E, Allan AC, Bowen J, Harvey I, Johnston J, Malnoy M, Troggio M, Perchepied L, Sawyer G, Wiedow C, Won K, Viola R, Hellens RP, Brewer L, Bus VGM, Schaffer RJ, Gardiner SE, Velasco R. The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS One 2014; 9:e92644. [PMID: 24699266 PMCID: PMC3974708 DOI: 10.1371/journal.pone.0092644] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 02/25/2014] [Indexed: 01/03/2023] Open
Abstract
We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malus × domestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/pyrus_communis/genome_v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development.
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Affiliation(s)
- David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Massimo Pindo
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | | | - Cecilia Deng
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Hilary Ireland
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mark Fiers
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Helge Dzierzon
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Alessandro Cestaro
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Paolo Fontana
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Luca Bianco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Ashley Lu
- Lincoln Research Centre, Plant & Food Research, Lincoln, New Zealand
| | - Roy Storey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Munazza Saeed
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Institute of Food, Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Sara Montanari
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Yoon Kyeong Kim
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Daniela Nicolini
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Simone Larger
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Erika Stefani
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Andrew C. Allan
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Judith Bowen
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Isaac Harvey
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Jason Johnston
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Mickael Malnoy
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Michela Troggio
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Laure Perchepied
- Institut de Recherche en Horticulture et Semences (IRHS), Institut National en Recherche Agronomique (INRA), Angers, France
| | - Greg Sawyer
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Claudia Wiedow
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Naju, Republic of Korea
| | - Roberto Viola
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
| | - Roger P. Hellens
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
| | - Lester Brewer
- Motueka Research Centre, Plant & Food Research, Motueka, New Zealand
| | - Vincent G. M. Bus
- Hawke's Bay Research Centre, Plant & Food Research, Havelock North, New Zealand
| | - Robert J. Schaffer
- Mount Albert Research Centre, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan E. Gardiner
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North, New Zealand
| | - Riccardo Velasco
- Istituto Agrario San Michele all'Adige (IASMA) Research and Innovation Centre, Foundation Edmund Mach (FEM), San Michele all' Adige, Trento, Italy
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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Nakasugi K, Crowhurst RN, Bally J, Wood CC, Hellens RP, Waterhouse PM. De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PLoS One 2013; 8:e59534. [PMID: 23555698 PMCID: PMC3610648 DOI: 10.1371/journal.pone.0059534] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/15/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. METHODOLOGY/RESULTS RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of 16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. CONCLUSIONS The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant.
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Affiliation(s)
- Kenlee Nakasugi
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Ross N. Crowhurst
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
| | - Julia Bally
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Craig C. Wood
- Commonwealth Scientific and Industrial Research Organisation–Plant Industry, Canberra, Australia
| | - Roger P. Hellens
- Mount Albert Research Centre, Plant and Food Research, Auckland, New Zealand
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14
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Chagné D, Lin-Wang K, Espley RV, Volz RK, How NM, Rouse S, Brendolise C, Carlisle CM, Kumar S, De Silva N, Micheletti D, McGhie T, Crowhurst RN, Storey RD, Velasco R, Hellens RP, Gardiner SE, Allan AC. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol 2013; 161:225-39. [PMID: 23096157 PMCID: PMC3532254 DOI: 10.1104/pp.112.206771] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 10/23/2012] [Indexed: 05/18/2023]
Abstract
Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity.
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Affiliation(s)
- David Chagné
- New Zealand Institute for Plant and Food Research Limited , Palmerston North Research Centre, Palmerston North 4442, New Zealand.
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15
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Naim F, Nakasugi K, Crowhurst RN, Hilario E, Zwart AB, Hellens RP, Taylor JM, Waterhouse PM, Wood CC. Advanced engineering of lipid metabolism in Nicotiana benthamiana using a draft genome and the V2 viral silencing-suppressor protein. PLoS One 2012; 7:e52717. [PMID: 23300750 PMCID: PMC3530501 DOI: 10.1371/journal.pone.0052717] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/20/2012] [Indexed: 01/05/2023] Open
Abstract
The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18∶1 to elongation reactions beginning with 18∶1 as substrate. These V2-based leaf assays produced ∼50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays.
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Affiliation(s)
- Fatima Naim
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Kenlee Nakasugi
- School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Ross N. Crowhurst
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Elena Hilario
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Alexander B. Zwart
- Mathematics, Informatics and Statistics, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Roger P. Hellens
- Breeding and Genomics, The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Auckland, New Zealand
| | - Jennifer M. Taylor
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Peter M. Waterhouse
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
- School of Molecular Bioscience, School of Biological Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Craig C. Wood
- Plant Industry, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
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Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 2012; 7:e31745. [PMID: 22363718 PMCID: PMC3283661 DOI: 10.1371/journal.pone.0031745] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023] Open
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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Affiliation(s)
- David Chagné
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Barbara Gilmore
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cindy Lawley
- Illumina Inc., Hayward, California, United States of America
| | - Stijn Vanderzande
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Roger P. Hellens
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Satish Kumar
- Plant and Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Alessandro Cestaro
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Jasper D. Rees
- Agricultural Research Council, Onderstepoort, South Africa
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Todd Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Susan E. Gardiner
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R. The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 2010; 42:833-9. [DOI: 10.1038/ng.654] [Citation(s) in RCA: 1538] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 08/03/2010] [Indexed: 11/09/2022]
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Fraser LG, Tsang GK, Datson PM, De Silva HN, Harvey CF, Gill GP, Crowhurst RN, McNeilage MA. A gene-rich linkage map in the dioecious species Actinidia chinensis (kiwifruit) reveals putative X/Y sex-determining chromosomes. BMC Genomics 2009; 10:102. [PMID: 19284545 PMCID: PMC2661093 DOI: 10.1186/1471-2164-10-102] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 03/10/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The genus Actinidia (kiwifruit) consists of woody, scrambling vines, native to China, and only recently propagated as a commercial crop. All species described are dioecious, but the genetic mechanism for sex-determination is unknown, as is the genetic basis for many of the cluster of characteristics making up the unique fruit. It is, however, an important crop in the New Zealand economy, and a classical breeding program would benefit greatly by knowledge of the trait alleles carried by both female and male parents. The application of marker assisted selection (MAS) in seedling populations would also aid the accurate and efficient development of novel fruit types for the market. RESULTS Gene-rich female, male and consensus linkage maps of the diploid species A. chinensis have been constructed with 644 microsatellite markers. The maps consist of twenty-nine linkage groups corresponding to the haploid number n = 29. We found that sex-linked sequence characterized amplified region (SCAR) markers and the 'Flower-sex' phenotype consistently mapped to a single linkage group, in a subtelomeric region, in a section of inconsistent marker order. The region also contained markers of expressed genes, some of unknown function. Recombination, assessed by allelic distribution and marker order stability, was, in the remainder of the linkage group, in accordance with other linkage groups. Fully informative markers to other genes in this linkage group identified the comparative linkage group in the female map, where recombination ratios determining marker order were similar to the autosomes. CONCLUSION We have created genetic linkage maps that define the 29 linkage groups of the haploid genome, and have revealed the position and extent of the sex-determining locus in A. chinensis. As all Actinidia species are dioecious, we suggest that the sex-determining loci of other Actinidia species will be similar to that region defined in our maps. As the extent of the non-recombining region is limited, our result supports the suggestion that the subtelomeric region of an autosome is in the early stages of developing the characteristics of a sex chromosome. The maps provide a reference of genetic information in Actinidia for use in genetic analysis and breeding programs.
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Affiliation(s)
- Lena G Fraser
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand.
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Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS. Development of a set of SNP markers present in expressed genes of the apple. Genomics 2008; 92:353-8. [PMID: 18721872 DOI: 10.1016/j.ygeno.2008.07.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 11/25/2022]
Abstract
Molecular markers associated with gene coding regions are useful tools for bridging functional and structural genomics. Due to their high abundance in plant genomes, single nucleotide polymorphisms (SNPs) are present within virtually all genomic regions, including most coding sequences. The objective of this study was to develop a set of SNPs for the apple by taking advantage of the wealth of genomics resources available for the apple, including a large collection of expressed sequenced tags (ESTs). Using bioinformatics tools, a search for SNPs within an EST database of approximately 350,000 sequences developed from a variety of apple accessions was conducted. This resulted in the identification of a total of 71,482 putative SNPs. As the apple genome is reported to be an ancient polyploid, attempts were made to verify whether those SNPs detected in silico were attributable either to allelic polymorphisms or to gene duplication or paralogous or homeologous sequence variations. To this end, a set of 464 PCR primer pairs was designed, PCR was amplified using two subsets of plants, and the PCR products were sequenced. The SNPs retrieved from these sequences were then mapped onto apple genetic maps, including a newly constructed map of a Royal Gala x A689-24 cross and a Malling 9 x Robusta 5, map using a bin mapping strategy. The SNP genotyping was performed using the high-resolution melting (HRM) technique. A total of 93 new markers containing 210 coding SNPs were successfully mapped. This new set of SNP markers for the apple offers new opportunities for understanding the genetic control of important horticultural traits using quantitative trait loci (QTL) or linkage disequilibrium analysis. These also serve as useful markers for aligning physical and genetic maps, and as potential transferable markers across the Rosaceae family.
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Affiliation(s)
- David Chagné
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, Palmerston North 4442, New Zealand
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Jordan MD, Stanley D, Marshall SDG, De Silva D, Crowhurst RN, Gleave AP, Greenwood DR, Newcomb RD. Expressed sequence tags and proteomics of antennae from the tortricid moth, Epiphyas postvittana. Insect Mol Biol 2008; 17:361-373. [PMID: 18651918 DOI: 10.1111/j.1365-2583.2008.00812.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Genomic and proteomic analyses of the antennae of the light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae) were undertaken to identify genes and proteins potentially involved in odorant and pheromone binding and turnover. An EST approach yielded 5739 sequences, comprising 808 contigs and 1545 singletons. InterPro and Blast analyses revealed members of families implicated in odorant and pheromone binding (PBPs, GOBPs, ABPXs and CSPs) and turnover (CXEs, GSTs, CYPs). Of the three pheromone binding proteins (PBPs) identified, two were more highly expressed at the RNA and protein levels in adult male antennae (EpPBP1, EpPBP3), while a third was more highly expressed in female antennae (EpPBP2). To identify proteins involved in the detection of sex-specific signals, differential 2D gel electrophoresis (pH 5-8) followed by mass spectrometry was conducted on antennal proteins from males versus females. Identified male-biased proteins included a pheromone binding protein, a porin, a short chain dehydrogenase/reductase, and a member of the takeout family.
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Affiliation(s)
- M D Jordan
- The Horticultural and Food Research Institute of New Zealand Limited (HortResearch), Auckland, New Zealand
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21
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Crowhurst RN, Gleave AP, MacRae EA, Ampomah-Dwamena C, Atkinson RG, Beuning LL, Bulley SM, Chagne D, Marsh KB, Matich AJ, Montefiori M, Newcomb RD, Schaffer RJ, Usadel B, Allan AC, Boldingh HL, Bowen JH, Davy MW, Eckloff R, Ferguson AR, Fraser LG, Gera E, Hellens RP, Janssen BJ, Klages K, Lo KR, MacDiarmid RM, Nain B, McNeilage MA, Rassam M, Richardson AC, Rikkerink EH, Ross GS, Schröder R, Snowden KC, Souleyre EJF, Templeton MD, Walton EF, Wang D, Wang MY, Wang YY, Wood M, Wu R, Yauk YK, Laing WA. Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening. BMC Genomics 2008; 9:351. [PMID: 18655731 PMCID: PMC2515324 DOI: 10.1186/1471-2164-9-351] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 07/27/2008] [Indexed: 11/13/2022] Open
Abstract
Background Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs). Results The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.
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Affiliation(s)
- Ross N Crowhurst
- The Horticultural and Food Research Institute of New Zealand, PB 92169, Auckland, New Zealand.
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Janssen BJ, Thodey K, Schaffer RJ, Alba R, Balakrishnan L, Bishop R, Bowen JH, Crowhurst RN, Gleave AP, Ledger S, McArtney S, Pichler FB, Snowden KC, Ward S. Global gene expression analysis of apple fruit development from the floral bud to ripe fruit. BMC Plant Biol 2008; 8:16. [PMID: 18990244 PMCID: PMC2287172 DOI: 10.1186/1471-2229-8-16] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 02/17/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45-55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple. RESULTS Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes. CONCLUSION Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.
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Affiliation(s)
- Bart J Janssen
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Kate Thodey
- John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Robert J Schaffer
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Rob Alba
- Boyce Thompson Institute for Plant Research, Tower Road, Cornell University Campus, Ithaca, NY 14853, USA
- Monsanto Company – O3D, Product Safety Center, 800 North Lindbergh Blvd., St. Louis, MO 63167, USA
| | | | - Rebecca Bishop
- 4 La Trobe Track, RD2 New Lynn, Karekare, Auckland, New Zealand
| | - Judith H Bowen
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Ross N Crowhurst
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Andrew P Gleave
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Susan Ledger
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Steve McArtney
- Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Centre, 455 Research Drive, Fletcher, NC 28732-9244, USA
| | - Franz B Pichler
- Microbial Ecology & Genomics Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Kimberley C Snowden
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Shayna Ward
- The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
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Simpson RM, Newcomb RD, Gatehouse HS, Crowhurst RN, Chagné D, Gatehouse LN, Markwick NP, Beuning LL, Murray C, Marshall SD, Yauk YK, Nain B, Wang YY, Gleave AP, Christeller JT. Expressed sequence tags from the midgut of Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae). Insect Mol Biol 2007; 16:675-690. [PMID: 18092997 DOI: 10.1111/j.1365-2583.2007.00763.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The midgut is a key tissue in insect science. Physiological roles include digestion and peritrophic membrane function, as well as being an important target for insecticides. We used an expressed sequence tag (EST) approach to identify candidate genes and gene families involved in these processes in the light brown apple moth, Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae). Two cDNA libraries were constructed from dissected midgut of third to fifth instar larvae. Clustering analysis of 6416 expressed sequence tags produced 1178 tentative unique genes comprising 725 tentative contigs and 453 singletons. The sequences show similar codon usage to sequences from other lepidopterans, a Kozak consensus sequence similar to Drosophila and single nucleotide polymorphisms (SNPs) were detected at a frequency of 1.35/kb. The identity of the most common Interpro families correlates well with major known functions of the midgut. Phylogenetic analysis was conducted on representative sequences from selected multigene families. Gene families include a broad range of digestive proteases, lipases and carbohydrases that appear to have degradative capacity against the major food components found in leaves, the diet of these larvae; and carboxylesterases, glutathione-S-transferases and cytochrome P450 monooxygenases, potentially involved in xenobiotic degradation. Two of the larger multigene families, serine proteases and lipases, expressed a high proportion of genes that are likely to be catalytically inactive.
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Affiliation(s)
- R M Simpson
- Horticulture and Food Research Institute, Palmerston North, New Zealand
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Schaffer RJ, Friel EN, Souleyre EJF, Bolitho K, Thodey K, Ledger S, Bowen JH, Ma JH, Nain B, Cohen D, Gleave AP, Crowhurst RN, Janssen BJ, Yao JL, Newcomb RD. A genomics approach reveals that aroma production in apple is controlled by ethylene predominantly at the final step in each biosynthetic pathway. Plant Physiol 2007; 144:1899-912. [PMID: 17556515 PMCID: PMC1949883 DOI: 10.1104/pp.106.093765] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ethylene is the major effector of ripening in many fleshy fruits. In apples (Malus x domestica) the addition of ethylene causes a climacteric burst of respiration, an increase in aroma, and softening of the flesh. We have generated a transgenic line of 'Royal Gala' apple that produces no detectable levels of ethylene using antisense ACC OXIDASE, resulting in apples with no ethylene-induced ripening attributes. In response to external ethylene these antisense fruits undergo a normal climacteric burst and produced increasing concentrations of ester, polypropanoid, and terpene volatile compounds over an 8-d period. A total of 186 candidate genes that might be involved in the production of these compounds were mined from expressed sequence tags databases and full sequence obtained. Expression patterns of 179 of these were assessed using a 15,720 oligonucleotide apple microarray. Based on sequence similarity and gene expression patterns we identified 17 candidate genes that are likely to be ethylene control points for aroma production in apple. While many of the biosynthetic steps in these pathways were represented by gene families containing two or more genes, expression patterns revealed that only a single member is typically regulated by ethylene. Only certain points within the aroma biosynthesis pathways were regulated by ethylene. Often the first step, and in all pathways the last steps, contained enzymes that were ethylene regulated. This analysis suggests that the initial and final enzymatic steps with the biosynthetic pathways are important transcriptional regulation points for aroma production in apple.
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Affiliation(s)
- Robert J Schaffer
- Horticulture and Food Research Institute of New Zealand, Mt. Albert, Auckland, New Zealand
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Chagné D, Carlisle CM, Blond C, Volz RK, Whitworth CJ, Oraguzie NC, Crowhurst RN, Allan AC, Espley RV, Hellens RP, Gardiner SE. Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple. BMC Genomics 2007; 8:212. [PMID: 17608951 PMCID: PMC1939713 DOI: 10.1186/1471-2164-8-212] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 07/03/2007] [Indexed: 12/02/2022] Open
Abstract
Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species.
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Affiliation(s)
- David Chagné
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Charmaine M Carlisle
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Céline Blond
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
| | - Richard K Volz
- HortResearch Hawke's Bay, PB 1401, Havelock North 4157, New Zealand
| | | | | | | | - Andrew C Allan
- HortResearch Mount Albert, PB 92169, Auckland 1142, New Zealand
| | | | - Roger P Hellens
- HortResearch Mount Albert, PB 92169, Auckland 1142, New Zealand
| | - Susan E Gardiner
- The Horticulture and Food Research Institute of New Zealand (HortResearch) Palmerston North, PB 11030, Manawatu Mail Centre, Palmerston North 4442, New Zealand
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Newcomb RD, Crowhurst RN, Gleave AP, Rikkerink EHA, Allan AC, Beuning LL, Bowen JH, Gera E, Jamieson KR, Janssen BJ, Laing WA, McArtney S, Nain B, Ross GS, Snowden KC, Souleyre EJF, Walton EF, Yauk YK. Analyses of expressed sequence tags from apple. Plant Physiol 2006; 141:147-66. [PMID: 16531485 PMCID: PMC1459330 DOI: 10.1104/pp.105.076208] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5'-untranslated region of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis (Arabidopsis thaliana) suggest instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop.
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Affiliation(s)
- Richard D Newcomb
- Horticultural and Food Research Institute of New Zealand Limited, Mt. Albert Research Centre, Auckland, New Zealand.
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Fraser LG, Harvey CF, Crowhurst RN, De Silva HN. EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 2004; 108:1010-6. [PMID: 15067386 DOI: 10.1007/s00122-003-1517-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 10/28/2003] [Indexed: 05/18/2023]
Abstract
To increase the speed and reduce the cost of constructing a genetic map of Actinidia species (kiwifruit), for use in both breeding and functional genomics programmes, we sampled microsatellites from expressed sequence tags (ESTs) to evaluate their frequency of occurrence and level of polymorphism. Perfect dinucleotide repeats were the microsatellites selected, and these were found to be numerous in both the 5' and 3' ends of the genes represented. The microsatellites were of various lengths, the majority being repeats with the pattern (CT)(n)/(GA)(n). One hundred and fifty microsatellites, each with more than 10 dinucleotide repeat units, were chosen as possible markers, and when these were amplified, 93.5% were found to be polymorphic and segregating in a mapping population, with 22.6% amplifying more than one locus. Four marker categories were identified. Fully informative markers made up 27% of the total, 36.2% were female informative, 25.8% were male informative and 10% partly informative. The mapping population was an intraspecific cross in the diploid species Actinidia chinensis, with parents chosen for their diversity in fruit and plant characteristics, and for their geographical separation. Linkage was tested using the software 'Joinmap' and a LOD value of 3. The distribution of the EST-based markers over the linkage groups obtained appeared to be random, taking into consideration the small sample size, that the number of linkage groups (31) exceeded the chromosome number of n=29, and that a number of markers were not assigned to any group. Some microsatellite markers which amplified more than one locus mapped to separate linkage groups. According to our study in A. chinensis, EST-derived microsatellites give large numbers of possible markers very quickly and at reasonable cost. The markers are highly polymorphic, segregate in the mapping population, and increase the value of the genomic map by providing some functional information.
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Affiliation(s)
- L G Fraser
- The Horticulture and Food Research Institute of New Zealand, 120 Mt Albert Road, Auckland, New Zealand.
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Hawthorne BT, Rees-George J, Crowhurst RN. Induction of cutinolytic esterase activity during saprophytic growth of cucurbit pathogens, Fusarium solani f. sp. cucurbitae races one and two (Nectria haematococca MPI and MPV, respectively). FEMS Microbiol Lett 2001; 194:135-41. [PMID: 11164297 DOI: 10.1111/j.1574-6968.2001.tb09458.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Cutins from fruit of Cucurbita maxima and Cucurbita moschata cultivars, apple and a C(16) alcohol (hexadecanol) were used to induce cutinolytic esterase activity during saprophytic growth of strains of the two cucurbit pathogens, Fusarium solani f. sp. cucurbitae, race 1 (Nectria haematococca mating population (MPI) and F. solani f. sp. cucurbitae, race 2 (MPV). Four strains of MPV and 11 strains of MPI were were included in the study. Although we were primarily interested in the two cucurbit pathogens (MPI and MPV), six strains of the pea pathogen F. solani f. sp. pisi (MPVI) were included to provide a comparison since most of the knowledge on cutinase activity in N. haematococca has come from a study of that group. Cutinolytic esterase was induced in all strains from both MPV and MPVI but was not detected in any of the 11 strains from MPI regardless of the induction conditions. The amount of cutinolytic esterase activity induced in the MPV strains differed according to the strain and both the source and the amount of cutin used in the induction medium. Information on the influence of cutin source and pH on the induction of cutinolytic esterase activity during saprophytic growth of strains from MPV demonstrates that the gene is regulated differently from that in MPVI.
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Affiliation(s)
- B T Hawthorne
- Molecular Genetics Group, Horticulture and Food Research Institute of New Zealand Ltd., Private Bag 92169, Auckland, New Zealand.
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Goldstein AL, Carpenter MA, Crowhurst RN, Stewart A. Identification of Coniothyrium minitansisolates using PCR amplification of a dispersed repetitive element. Mycologia 2000. [DOI: 10.1080/00275514.2000.12061129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Alan L. Goldstein
- Soil, Plant and Ecological Sciences Division, P.O. Box 84, Lincoln University, Canterbury, New Zealand
| | - Margaret A. Carpenter
- Soil, Plant and Ecological Sciences Division, P.O. Box 84, Lincoln University, Canterbury, New Zealand
| | - Ross N. Crowhurst
- Molecular Genetics Group, The Horticulture and Food Research Institute of New Zealand Ltd., Mt. Albert, Auckland, New Zealand
| | - Alison Stewart
- Soil, Plant and Ecological Sciences Division, P.O. Box 84, Lincoln University, Canterbury, New Zealand
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Goldstein AL, Carpenter MA, Crowhurst RN, Stewart A. Identification of Coniothyrium minitans Isolates Using PCR Amplification of a Dispersed Repetitive Element. Mycologia 2000. [DOI: 10.2307/3761449] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Crowhurst RN, Binnie SJ, Bowen JK, Hawthorne BT, Plummer KM, Rees-George J, Rikkerink EH, Templeton MD. Effect of disruption of a cutinase gene (cutA) on virulence and tissue specificity of Fusarium solani f. sp. cucurbitae race 2 toward Cucurbita maxima and C. moschata. Mol Plant Microbe Interact 1997; 10:355-368. [PMID: 9100380 DOI: 10.1094/mpmi.1997.10.3.355] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A 3.9-kb genomic DNA fragment from the cucurbit pathogen Fusarium solani f. sp. cucurbitae race 2 was cloned. Sequence analysis revealed an open reading frame of 690 nucleotides interrupted by a single 51-bp intron. The nucleotide and predicted amino acid sequences showed 92 and 98% identity, respectively, to those of the cutA gene of the pea pathogen F. solani f. sp. pisi. A gene replacement vector was constructed and used to generate cutA- mutants that were detected with a polymerase chain reaction (PCR) assay. Seventy-one cutA- mutants were identified among the 416 transformants screened. Vector integration was assessed by Southern analysis in 23 of these mutants. PCR and Southern analysis data showed the level of homologous integration was 14%. Disruption of the cutA locus in mutants was confirmed by RNA gel blot hybridization. Neither virulence on Cucurbita maxima cv. Delica at any of six different inoculum concentrations, nor pathogenicity on intact fruit of four different species or cultivars of cucurbit or hypocotyl tissue of C. maxima cv. Crown, was found to be affected by disruption of the cutA gene.
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Affiliation(s)
- R N Crowhurst
- Molecular Genetics Group, Horticulture and Food Research Institute of New Zealand Ltd., Auckland.
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Bowen JK, Templeton MD, Sharrock KR, Crowhurst RN, Rikkerink EH. Gene inactivation in the plant pathogen Glomerella cingulata: three strategies for the disruption of the pectin lyase gene pnlA. Mol Gen Genet 1995; 246:196-205. [PMID: 7862090 DOI: 10.1007/bf00294682] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The feasibility of performing routine transformation-mediated mutagenesis in Glomerella cingulata was analysed by adopting three one-step gene disruption strategies targeted at the pectin lyase gene pnlA. The efficiencies of disruption following transformation with gene replacement- or gene truncation-disruption vectors were compared. To effect replacement-disruption, G. cingulata was transformed with a vector carrying DNA from the pnlA locus in which the majority of the coding sequence had been replaced by the gene for hygromycin B resistance. Two of the five transformants investigated contained an inactivated pnlA gene (pnlA-); both also contained ectopically integrated vector sequences. The efficacy of gene disruption by transformation with two gene truncation-disruption vectors was also assessed. Both vectors carried at 5' and 3' truncated copy of the pnlA coding sequence, adjacent to the gene for hygromycin B resistance. The promoter sequences controlling the selectable marker differed in the two vectors. In one vector the homologous G. cingulata gpdA promoter controlled hygromycin B phosphotransferase expression (homologous truncation vector), whereas in the second vector promoter elements were from the Aspergillus nidulans gpdA gene (heterologous truncation vector). Following transformation with the homologous truncation vector, nine transformants were analysed by Southern hybridisation; no transformants contained a disrupted pnlA gene. Of nineteen heterologous truncation vector transformants, three contained a disrupted pnlA gene; Southern analysis revealed single integrations of vector sequence at pnlA in two of these transformants. pnlA mRNA was not detected by Northern hybridisation in pnlA- transformants. pnlA- transformants failed to produce a PNLA protein with a pI identical to one normally detected in wild-type isolates by silver and activity staining of isoelectric focussing gels. Pathogenesis on Capsicum and apple was unaffected by disruption of the pnlA gene, indicating that the corresponding gene product, PNLA, is not essential for pathogenicity. Gene disruption is a feasible method for selectively mutating defined loci in G. cingulata for functional analysis of the corresponding gene products.
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Affiliation(s)
- J K Bowen
- Horticulture and Food Research Institute of New Zealand Ltd., Mt. Albert Research Centre, Auckland
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Crowhurst RN, King FY, Hawthorne BT, Sanderson FR, Choi-Pheng Y. RAPD characterization of Fusarium oxysporum associated with wilt of angsana (Pterocarpus indicus) in Singapore. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0953-7562(09)80310-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Templeton MD, Sharrock KR, Bowen JK, Crowhurst RN, Rikkerink EH. The pectin lyase-encoding gene (pnl) family from Glomerella cingulata: characterization of pnlA and its expression in yeast. Gene 1994; 142:141-6. [PMID: 8181749 DOI: 10.1016/0378-1119(94)90369-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Oligodeoxyribonucleotide primers were designed from conserved amino acid (aa) sequences between pectin lyase D (PNLD) from Aspergillus niger and pectate lyases A and E (PELA/E) from Erwinia chrysanthemi. The polymerase chain reaction (PCR) was used with these primers to amplify genomic DNA from the plant pathogenic fungus Glomerella cingulata. Three different 220-bp fragments with homology to PNL-encoding genes from A. niger, and a 320-bp fragment with homology to PEL-encoding genes from Nicotiana tabacum and E. carotovora were cloned. One of the 220-bp PCR products (designated pnlA) was used as a probe to isolate a PNL-encoding gene from a lambda genomic DNA library prepared from G. cingulata. Nucleotide (nt) sequence data revealed that this gene has seven exons and codes for a putative 380-aa protein. The nt sequence of a cDNA clone, prepared using PCR, confirmed the presence of the six introns. The positions of the introns were different from the sites of the five introns present in the three PNL-encoding genes previously sequenced from A. niger. PNLA was synthesised in yeast by cloning the cDNA into the expression vector, pEMBLYex-4, and enzymatically active protein was secreted into the culture medium. Significantly higher expression was achieved when the context of the start codon, CACCATG, was mutated to CAAAATG, a consensus sequence commonly found in highly expressed yeast genes. The produced protein had an isoelectric point (pI) of 9.4, the same as that for the G. cingulata pnlA product.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M D Templeton
- Molecular Genetics Group, Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Auckland
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Rikkerink EH, Solon SL, Crowhurst RN, Templeton MD. Integration of vectors by homologous recombination in the plant pathogen Glomerella cingulata. Curr Genet 1994; 25:202-8. [PMID: 7923405 DOI: 10.1007/bf00357163] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
An homologous transformation system has been developed for the plant pathogenic fungus Glomerella cingulata (Colletotrichum gloeosporioides). A transformation vector containing the G. cingulata gpdA promoter fused to the hygromycin phosphotransferase gene was constructed. Southern analyses indicated that this vector integrated at single sites in most transformants. A novel method of PCR amplification across the recombination junction point indicated that the integration event occurred by homologous recombination in more than 95% of the transformants. Deletion studies demonstrated that 505 bp (the minimum length of homologous promoter DNA analysed which was still capable of promoter function) was sufficient to target integration events. Homologous integration of the vector resulted in duplication of the gdpA promoter region. When transformants were grown without selective pressure, a high incidence of vector excision by recombination between the duplicated regions was evident. The significance of these recombination characteristics is discussed with reference to the feasibility of performing gene disruption experiments.
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Affiliation(s)
- E H Rikkerink
- Molecular Genetics Group, Horticulture and Food Research Institute of New Zealand Ltd., Mount Albert Research Centre, Auckland
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Templeton MD, Rikkerink EH, Solon SL, Crowhurst RN. Cloning and molecular characterization of the glyceraldehyde-3-phosphate dehydrogenase-encoding gene and cDNA from the plant pathogenic fungus Glomerella cingulata. Gene X 1992; 122:225-30. [PMID: 1452034 DOI: 10.1016/0378-1119(92)90055-t] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The glyceraldehyde-3-phosphate dehydrogenase gene (gpdA) has been identified from a genomic DNA library prepared from the plant pathogenic fungus Glomerella cingulata. Nucleotide sequence data revealed that this gene codes for a putative 338-amino-acid protein encoded by two exons of 129 and 885 bp, separated by an intron 216 bp long. The 5' leader sequence is also spliced by an intron of 156 bp. A cDNA clone was prepared using the polymerase chain reaction, the sequence of which was used to confirm the presence of the intron in the coding sequence and the splicing of the 5' leader sequence. The transcriptional start point (tsp) was mapped at -253 nt from the site of the initiation of translation by primer extension and is adjacent to a 42-bp pyrimidine-rich region. The general structure of the 5' flanking region shows similarities to gpdA from Aspergillus nidulans. The putative protein product is 71-86% identical at the aa level to GPDs from Aspergillus nidulans, Cryphonectria parasitica, Curvularia lunata, Podospora anserina and Ustilago maydis.
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Affiliation(s)
- M D Templeton
- Molecular Genetics Group, Horticulture and Food Research Institute, New Zealand Ltd., Mt. Albert, Auckland
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Crowhurst RN, Rees-George J, Rikkerink EH, Templeton MD. High efficiency transformation of Fusarium solani f. sp. cucurbitae race 2 (mating population V). Curr Genet 1992; 21:463-9. [PMID: 1617735 DOI: 10.1007/bf00351656] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A cosmid vector, suitable for library construction and DNA transformation in filamentous fungi, has been constructed and a reliable and highly efficient PEG-mediated DNA transformation system for F. solani f. sp. cucurbitae, based on resistance to hygromycin B, has been developed for use with this vector. This transformation system yielded 10(4) transformants per micrograms of DNA when using 10(7) protoplasts. Factors important in achieving high efficiency included: the maintenance of an osmoticum in all transformation steps, PEG 4000 concentration, and the ratio of transforming vector DNA to protoplasts. Approximately 60% of transformants stably integrated vector DNA. Molecular analysis revealed multiple copies of the plasmid integrated into the genome at one or more sites. The frequency of transformation achieved will facilitate the isolation of genes from this fungus by complementation.
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Crowhurst RN, Hawthorne BT, Rikkerink EH, Templeton MD. Differentiation of Fusarium solani f. sp. cucurbitae races 1 and 2 by random amplification of polymorphic DNA. Curr Genet 1991; 20:391-6. [PMID: 1807830 DOI: 10.1007/bf00317067] [Citation(s) in RCA: 172] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have used a PCR-based technique, involving the random amplification of polymorphic DNA (RAPD), to assess genome variability between 21 isolates from F. solani f. sp. cucurbitae races 1 and 2. Based on RAPD marker patterns the isolates fell into two distinct groups corresponding to mating populations MPI and MPV. Four isolates that could not be assigned to one or other mating population by traditional means were distinguished by RAPD patterns. Seven polymorphic RAPD products were used to probe Southern blots of MPI and MPV genomic DNA. Six of the seven probes hybridized to single-copy sequences and five of the seven probes showed specificity for one or other mating population. We suggest that not only is the technique a rapid and reliable tool for isolate-typing of fungi but it also provides a rapid method for obtaining species- or race-specific hybridization probes.
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Crowhurst RN, Gardner RC. A genome-specific repeat sequence from kiwifruit (Actinidia deliciosa var. deliciosa). Theor Appl Genet 1991; 81:71-78. [PMID: 24221161 DOI: 10.1007/bf00226114] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/1990] [Accepted: 07/13/1990] [Indexed: 06/02/2023]
Abstract
Six members of a family of moderately repetitive DNA sequences from kiwifruit (Actinidia deliciosa var. deliciosa) have been cloned and characterized. The repeat family is composed of elements that have a unit length of 463 bp, are highly methylated, occur in tandem arrays of at least 50 kb in length, and constitute about 0.5% of the kiwifruit genome. Individual elements diverge in nucleotide sequence by up to 5%, which suggests that the repeat sequence is evolving rapidly. Homologous sequences were found in A. deliciosa var. chlorocarpa. The repeat sequence was not found under low stringency hybridization conditions in the diploid A. chinensis, the species most closely related to the hexaploid kiwifruit, or in eight other Actinidia species. However, homologous repeats were detected in a tetraploid species, A. chrysantha. The results provide the first molecular evidence to suggest that kiwifruit may be an allopolyploid species.
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Affiliation(s)
- R N Crowhurst
- Centre for Gene Technology, Department of Cellular and Molecular Biology, University of Auckland, Private Bag, Auckland, New Zealand
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