Emerging Genomics of Angiosperm Trees
- First Online:
Genome sequence assemblies of many angiosperm trees used in forestry are now emerging, in addition to the well-characterised genomes of black poplar and eucalyptus reviewed in previous chapters of this book. Whilst the number of published genomes of angiosperm forest trees lags behind that of angiosperm trees grown commercially for fruit or nuts, many new projects are underway. This is aided by the ever-decreasing cost of DNA sequencing technologies and has diverse motivations including tree improvement, ecological and evolutionary studies. In this chapter, we briefly review a number of recent whole genome projects including Chinese chestnut, European ash, dwarf birch, pedunculate oak, purple willow and shrub willow. We also describe new projects not yet in the public domain or with non-genomic data, and list various online resources where data and information can be accessed. We discuss potential future steps in improving genome assemblies, and the uses of such information in fields such as genomic selection to assist tree breeding.
KeywordsGenome sequencing Angiosperm Tree Breeding Transcriptomics
- Carlson JE. The chestnut genome project. In: Plant and animal genome XXII conference. Plant and Animal Genome. 2014. https://pag.confex.com/pag/xxii/webprogram/Paper9777.html.
- Carlson CH, Gouker FE, Serapiglia MJ, Tang H, Krishnakumar V, Town CD, Tuskan GA, et al. Annotation of the Salix purpurea L. genome and gene families important for biomass production. In: Plant and animal genome XXII conference. Plant and Animal Genome. 2014. https://pag.confex.com/pag/xxii/webprogram/Paper12085.html.
- Carlson CH, Gouker FE, DiFazio S, Zhou R, Smart L. High-resolution mapping of biomass-related traits in shrub willow (Salix purpurea L.). In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper21612.html.
- Cruz F, Julca I, Gómez-Garrido J, Loska D, Marcet-Houben M, Cano E, Galán B, et al. Genome sequence of the olive tree, Olea europaea. GigaScience. 2016;5:29.Google Scholar
- Faivre-Rampant P, Lesur I, Boussardon C, Bitton F, Bodénès C, Le Provost G, Bergès H, Fluch S, Kremer A, Plomion C. Analysis of BAC end sequences in oak, providing insights into the composition of the genome of this keystone species. BMC Genomics. 2011;12:292.CrossRefPubMedPubMedCentralGoogle Scholar
- Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P. Oxford Nanopore sequencing and de novo assembly of a eukaryotic genome. BioRxiv. 2015. www.biorxiv.org, http://biorxiv.org/content/early/2015/01/06/013490.short.
- Gouker FE, Zhou R, Evans L, DiFazio S, Bubner B, Zander M, Smart L. Genotypic-phenotypic variation and marker-based heritability estimates of a shrub willow (Salix purpurea) association population. In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper19730.html.
- Hebard FV, Islam-Faridi N, Staton ME, Georgi L. Biotechnology of trees: chestnut. In: Tree biotechnology. Boca Raton: CRC Press; 2014. p. 1.Google Scholar
- Helm D. Natural capital: valuing the planet. New Haven: Yale University Press; 2015.Google Scholar
- Kafkas S. Whole genome sequencing and high density genetic maps in pistachio reveal a large non-recombining region of sex chromosomes. In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper21642.html.
- Kubisiak TL, Nelson CD, Staton ME, Zhebentyayeva T, Smith C, Olukolu BA, Fang G-C, et al. A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica). Tree Genet Genomes. 2013;9(2):557–71.CrossRefGoogle Scholar
- LaBonte N, Woeste KE. Exploring patterns of sequence variation in regions associated with chestnut blight resistance using whole-genome resequencing of Chinese chestnut (Castanea mollissima). In: Plant and animal genome XXIV conference. Plant and Animal Genome. 2016. https://pag.confex.com/pag/xxiv/webprogram/Paper20702.html.
- Martínez-García PJ, Crepeau M, Puiu D, Gonzalez-Ibeas D, Stevens K, Whalen J, Butterfield T, et al. The genome sequence of walnut (Juglans regia L.) Cv ‘Chandler’. In: Plant and animal genome XXIII conference. Plant and Animal Genome. 2015. https://pag.confex.com/pag/xxiii/webprogram/Paper14583.html.
- Rajaraman S, Salojärvi JT. Silver birch – a model for tree genetics? In: Plant and animal genome XXIII. 2015. https://pag.confex.com/pag/xxiii/webprogram/Paper15896.html.
- Resende MDV, Resende Jr MFR, Sansaloni CP, Petroli CD, Missiaggia AA, Aguiar AM, Abad JM, et al. Genomic selection for growth and wood quality in eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol. 2012;194(1):116–28.CrossRefPubMedGoogle Scholar
- Rowley ER, Genomic resource development for European hazelnut (Corylus avellana L.) PhD Thesis, Oregon State University. 2016. http://hdl.handle.net/1957/59368.
- Singh R, Ong-Abdullah M, Low ETL, Manaf MAA, Rosli R, Nookiah R, Ooi LC, et al. Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature. 2013;500(7462):335–9.Google Scholar
- Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, et al. Genome sequence and genetic diversity of European ash trees. Nature. In press, doi:10.1038/nature20786.