Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

Bayly, Michael J.; Rigault, Philippe; Spokevicius, Antanas; Ladiges, Pauline Y.; Ades, Peter K.; Anderson, Charlotte; Bossinger, Gerd; Merchant, Andrew; Udovicic, Frank; Woodrow, Ian E.; Tibbits, Josquin

doi:10.1016/j.ympev.2013.07.006

Cited by 98 publications

(78 citation statements)

References 72 publications

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“…Numerous studies have highlighted the issue of incongruence between phylogenies based on chloroplast and nuclear DNA (e.g. Soltis and Kuzoff 1995;Kim and Donoghue 2008;Wang et al 2011;Yu et al 2013;Govindarajulu et al 2015) and, therefore, differences between the findings of Bayly et al (2013) and the present study (based on DArT markers, which are predominantly nuclear) are not surprising. McKinnon et al (1999) found extensive sharing of chloroplast DNA haplotypes among sympatric species from subgenus Eucalyptus in Tasmania, which showed a clear correlation with geographic patterns rather than phylogenetic relationships.…”

Section: Gene Flow and Hybridisationmentioning

confidence: 44%

“…Bayly et al (2013) used whole chloroplast genome sequences to construct a phylogeny of 39 eucalypt species, with many branches having 97-100% bootstrap support. Another technique that has recently been used in Eucalyptus is Diversity Arrays Technology (DArT) (Hudson et al 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Eucalyptus regnans, E. obliqua, E. triflora) have been included in molecular Phylogenomics of green ashes Australian Systematic Botanyphylogenies over the past 10 years (Bayly and Ladiges 2007;Steane et al 2011;Bayly et al 2013), there has been no broader study of the green ash eucalypts using these more advanced techniques. Prober et al (1990) used allozyme data to investigate diversity in the green ashes, and this revealed low differentiation among taxa and many relationships that were not consistent with those derived from morphological characters.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Rutherford¹,

Wilson²,

Rossetto³

et al. 2015

Aust. Systematic Bot.

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Abstract. Eucalyptus is a genus that occurs in a range of habitats in Australia, Papua New Guinea, Timor, Sulawesi and the Philippines, with several species being used as sources of timber and fibre. However, despite its ecological and commercial significance, understanding its evolutionary history remains a challenge. The focus of the present study is the green ashes (subgenus Eucalyptus section Eucalyptus). Although previous studies, based primarily on morphology, suggest that the green ashes form a monophyletic group, there has been disagreement concerning the divergence of taxa. The present study aims to estimate the phylogeny of the green ashes and closely related eucalypts (37 taxa from over 50 locations in south-eastern Australia), using genome-wide analyses based on Diversity Arrays Technology (DArT). Results of analyses were similar in topology and consistent with previous phylogenies based on sequence data. Many of the relationships supported those proposed by earlier workers. However, other relationships, particularly of taxa within the Sydney region and Blue Mountains, were not consistent with previous classifications. These findings raise important questions concerning how we define species and discern relationships in Eucalyptus and may have implications for other plant species, particularly those with a complex evolutionary history where hybridisation and recombination have occurred.

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Section: Gene Flow and Hybridisationmentioning

confidence: 44%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Rutherford¹,

Wilson²,

Rossetto³

et al. 2015

Aust. Systematic Bot.

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“…The first principal component explained 87% of variation between the analysed materials, Bayly et al 2013). Wood density of the species also had an influence on spectra.…”

Section: Near-infrared Spectroscopymentioning

confidence: 98%

Use of Visible and Near-Infrared Spectroscopy for Discrimination of Eucalypt Species by Examination of Solid Samples

Nisgoski¹,

Muniz²,

Gonçalves³

et al. 2017

JTFS

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Eucalypt species have high importance in the forestry sector in Brazil. The wood has wide range of uses, including pulp, charcoal, plywood panels and treated boards. However, eucalypt species are hard to identify in lumber, which can cause problems in industrial use. So, the aim of this study was to combine visible and near-infrared spectroscopy to discriminate wood samples of two Corymbia spp. and five Eucalyptus spp. Visible spectroscopy was performed according to the CIELab standard. The data were analysed using descriptive statistics and regression analysis. Near-infrared analyses were based on ASTM E1655-05. The data were analysed with the Unscrambler X chemometric program, in the raw form and after pre-processing with second derivative of Savitzky-Golay. Visible and near-infrared spectroscopy can be successfully applied to separate Eucalyptus and Corymbia species. In the visible spectroscopic analyses, it was possible to separate the wood samples into two colour groups, i.e. red/rose and grey/yellow/brown. In the near-infrared spectra it was possible to discriminate samples, and three groups associated with density of the species were formed. Both techniques were appropriate to distinguish species and their industrial use might solve practical problems.

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“…27 The cp region provides a barcode that can be effectively implemented to study the associations in specific plant groups. 28,29 As sequencing technology and bioinformatics continue to advance, complete plastome sequencing has revolutionized the technique of barcoding, which is termed as "Super-barcodes". 23 These plastid-genome-based species classification and identification have been progressively accepted by taxonomists.…”

mentioning

confidence: 99%

DNA barcoding: a genomic-based tool for authentication of phytomedicinals and its products

Balachandran¹,

Saravanan²,

Ramalingam³

2015

BTAT

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DNA barcoding helps to identify the plant materials based on short, standardized gene sequences in a rapid, accurate, and cost-effective manner. Recent reports reveal that DNA barcoding can be used for the assignment of unknown specimens to a taxonomic group, authentic identification of phytomedicinals, and in plant biodiversity conservation. Research indicates that there is no single universal barcode candidate for identification of all plant groups. Hence, comparative analysis of plant barcode loci is essential for choosing a best candidate for authenticating particular medicinal plant genus/families. Currently, both chloroplast/nuclear regions are used as universal barcodes for the authentication of phytomedicinals. A recent advance in genomics has further enhanced the progress in DNA barcoding of plants by the introduction of high-throughput techniques like next generation sequencing, which has paved the way for complete plastome sequencing that is now termed as super-barcodes. These approaches could improve the traditional ethno-botanical and scientific knowledge of phytomedicinals and their safe use. Hence, current focus is on the investigation of phytomedicinals and herbal product integrity and authenticity through DNA barcoding with the goal of protecting consumers from potential health risks associated with product substitution and contamination.

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Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

Cited by 98 publications

References 72 publications

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Phylogenomics of the green ash eucalypts (Myrtaceae): a tale of reticulate evolution and misidentification

Use of Visible and Near-Infrared Spectroscopy for Discrimination of Eucalypt Species by Examination of Solid Samples

DNA barcoding: a genomic-based tool for authentication of phytomedicinals and its products

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