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Koot E, Arnst E, Taane M, Goldsmith K, Thrimawithana A, Reihana K, González-Martínez SC, Goldsmith V, Houliston G, Chagné D. Genome-wide patterns of genetic diversity, population structure and demographic history in mānuka (Leptospermum scoparium) growing on indigenous Māori land. Hortic Res 2022; 9:uhab012. [PMID: 35039864 PMCID: PMC8771449 DOI: 10.1093/hr/uhab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 06/14/2023]
Abstract
Leptospermum scoparium J. R. Forst et G. Forst, known as mānuka by Māori, the indigenous people of Aotearoa (New Zealand), is a culturally and economically significant shrub species, native to New Zealand and Australia. Chemical, morphological and phylogenetic studies have indicated geographical variation of mānuka across its range in New Zealand, and genetic differentiation between New Zealand and Australia. We used pooled whole genome re-sequencing of 76 L. scoparium and outgroup populations from New Zealand and Australia to compile a dataset totalling ~2.5 million SNPs. We explored the genetic structure and relatedness of L. scoparium across New Zealand, and between populations in New Zealand and Australia, as well as the complex demographic history of this species. Our population genomic investigation suggests there are five geographically distinct mānuka gene pools within New Zealand, with evidence of gene flow occurring between these pools. Demographic modelling suggests three of these gene pools have undergone expansion events, whilst the evolutionary histories of the remaining two have been subjected to contractions. Furthermore, mānuka populations in New Zealand are genetically distinct from populations in Australia, with coalescent modelling suggesting these two clades diverged ~9-12 million years ago. We discuss the evolutionary history of this species and the benefits of using pool-seq for such studies. Our research will support the management and conservation of mānuka by landowners, particularly Māori, and the development of a provenance story for the branding of mānuka based products.
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Affiliation(s)
- Emily Koot
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | - Elise Arnst
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - Melissa Taane
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
| | | | | | - Kiri Reihana
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | | | | | - Gary Houliston
- Manaaki Whenua Landcare Research, 54 Gerald St, Lincoln 7608, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited (Plant & Food Research), Batchelar Rd, Palmerston North 4410, New Zealand
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McCartney AM, Hilario E, Choi S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D. An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome. Mol Ecol Resour 2021; 21:2125-2144. [PMID: 33955186 PMCID: PMC8362059 DOI: 10.1111/1755-0998.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/23/2020] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022]
Abstract
We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths but perhaps lower coverage constructed more contiguous, kmers and gene-complete assemblies than short read length input data with higher coverage. The final genome assembly was constructed into 14 pseudochromosomes using an initial flye long read assembly, a racon/medaka/pilon combined polishing strategy, salsa2 and allhic scaffolding, juicebox curation, and Macadamia linkage map validation. We highlighted the importance of developing assembly workflows based on the volume and read length of sequencing data and established a robust set of quality metrics for generating high-quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by Hi-C data and that assembly scaffolding was more successful when the underlying contig assembly was of higher accuracy. These findings provide insight into how quality assessment tools can be implemented throughout genome assembly pipelines to inform the de novo reconstruction of a high-quality genome assembly for nonmodel organisms.
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Affiliation(s)
- Ann M. McCartney
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
| | - Elena Hilario
- Genomics AotearoaDunedinNew Zealand
- The New Zealand Institute for Plant and Food Research (Plant & Food Research)SandringhamNew Zealand
| | - Seung‐Sub Choi
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Joseph Guhlin
- Genomics AotearoaDunedinNew Zealand
- University of OtagoDunedinNew Zealand
| | - Jessica M. Prebble
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Gary Houliston
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Thomas R. Buckley
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - David Chagné
- Genomics AotearoaDunedinNew Zealand
- Plant & Food ResearchFitzherbert, Palmerston NorthNew Zealand
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Smith GR, Ganley BJ, Chagné D, Nadarajan J, Pathirana RN, Ryan J, Arnst EA, Sutherland R, Soewarto J, Houliston G, Marsh AT, Koot E, Carnegie AJ, Menzies T, Lee DJ, Shuey LS, Pegg GS. Resistance of New Zealand Provenance Leptospermum scoparium, Kunzea robusta, Kunzea linearis, and Metrosideros excelsa to Austropuccinia psidii. Plant Dis 2020; 104:1771-1780. [PMID: 32272027 DOI: 10.1094/pdis-11-19-2302-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Resistance to the pandemic strain of Austropuccinia psidii was identified in New Zealand provenance Leptospermum scoparium, Kunzea robusta, and K. linearis plants. Only 1 Metrosideros excelsa-resistant plant was found (of the 570 tested) and no resistant plants of either Lophomyrtus bullata or L. obcordata were found. Three types of resistance were identified in Leptospermum scoparium. The first two, a putative immune response and a hypersensitive response, are leaf resistance mechanisms found in other myrtaceous species while on the lateral and main stems a putative immune stem resistance was also observed. Both leaf and stem infection were found on K. robusta and K. linearis plants as well as branch tip dieback that developed on almost 50% of the plants. L. scoparium, K. robusta, and K. linearis are the first myrtaceous species where consistent infection of stems has been observed in artificial inoculation trials. This new finding and the first observation of significant branch tip dieback of plants of the two Kunzea spp. resulted in the development of two new myrtle rust disease severity assessment scales. Significant seed family and provenance effects were found in L. scoparium, K. robusta, and K. linearis: some families produced significantly more plants with leaf, stem, and (in Kunzea spp.) branch tip dieback resistance, and provenances provided different percentages of resistant families and plants. The distribution of the disease symptoms on plants from the same seed family, and between plants from different seed families, suggested that the leaf, stem, and branch tip dieback resistances were the result of independent disease resistance mechanisms.
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Affiliation(s)
- Grant R Smith
- The New Zealand Institute for Plant and Food Research Limited, Lincoln 7608, New Zealand
| | - Beccy J Ganley
- The New Zealand Institute for Plant and Food Research Limited, Te Puke 3182, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Jayanthi Nadarajan
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Ranjith N Pathirana
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Julie Ryan
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Elise A Arnst
- Manaaki Whenua Landcare Research, Lincoln 7608, New Zealand
| | | | | | - Gary Houliston
- Manaaki Whenua Landcare Research, Lincoln 7608, New Zealand
| | - Alby T Marsh
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4410, New Zealand
| | - Angus J Carnegie
- Forest Science, Department of Primary Industries-Forestry, Parramatta, NSW 2150 Australia
| | - Tracey Menzies
- The Queensland Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - David J Lee
- The University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia
| | - Louise S Shuey
- The Queensland Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
| | - Geoff S Pegg
- The Queensland Department of Agriculture and Fisheries, Brisbane, Queensland 4001, Australia
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Peltzer DA, Bellingham PJ, Dickie IA, Houliston G, Hulme PE, Lyver PO, McGlone M, Richardson SJ, Wood J. Scale and complexity implications of making New Zealand predator-free by 2050. J R Soc N Z 2019. [DOI: 10.1080/03036758.2019.1653940] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | | | - Ian A. Dickie
- Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Philip E. Hulme
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
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Heenan P, Mitchell C, Houliston G. Genetic Variation and Hybridisation among Eight Species of kōwhai (Sophora: Fabaceae) from New Zealand Revealed by Microsatellite Markers. Genes (Basel) 2018; 9:genes9020111. [PMID: 29461510 PMCID: PMC5852607 DOI: 10.3390/genes9020111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/12/2018] [Accepted: 02/16/2018] [Indexed: 11/19/2022] Open
Abstract
We analysed nine microsatellite markers for 626 individuals representing the geographic range of eight closely related endemic New Zealand species of Sophora. Structure analysis identified the optimal K value as seven, with samples identified as Sophora chathamica, Sophora fulvida, Sophora longicarinata, and Sophora prostrata retrieved as well-defined groups. The remaining samples formed less resolved groups referable to Sophora tetraptera and Sophora godleyi, with Sophora microphylla and Sophora molloyi forming the seventh group. Our data suggest that considerable admixture occurs and this is most likely the result of hybridisation or introgression. S. fulvida shows admixture with the sympatric S. chathamica, and the widespread S. microphylla exhibits admixture with the sympatric S. godleyi, S. molloyi, and S. tetraptera.
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Affiliation(s)
- Peter Heenan
- Research Associate, Allan Herbarium, Landcare Research, PO Box 40, Lincoln 7640, New Zealand.
| | | | - Gary Houliston
- Landcare Research, PO Box 40, Lincoln 7640, New Zealand.
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