Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences

Neves, Susana S.; Forrest, Laura L.

doi:10.1007/978-1-61779-276-2_10

Cited by 9 publications

(7 citation statements)

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“…The ITS region has a tendency to be homogenized for its sequence variation in concerted evolution and is easily amplified in the majority of plant species. These properties have caused the ITS region to gain wide popularity in modern plant phylogenetic studies ( Neves and Forrest, 2011 ). The first report to utilize ITS to evaluate phylogeny relationships at the nuclear level among agarwood-producing species was carried out by Lee and Mohamed (2016a) , and comprised seven Aquilaria species of Malaysia and Thailand origins, followed by a phylogeny study on the genetic diversity of eight different species from Aquilaria and Gyrinops from Indonesia ( Lee et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

et al. 2018

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The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS) sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35–2.23 pg). Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history.

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Section: Discussionmentioning

confidence: 99%

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

et al. 2018

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“…Those algorithms that utilize such sequence data to construct phylogenetic trees have been recently developed [31–33]. For example, using data matrix constructed based on assembled contigs from RNA-Seq reads, a robust phylogeny of 10 mosquito species was constructed [33].…”

Section: Introductionmentioning

confidence: 99%

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications

et al. 2015

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BackgroundThe genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the genus Flaveria contains 21 of the 23 known Flaveria species and has been previously constructed using a combination of morphological data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnL-F).ResultsHere we developed a new strategy to update the phylogenetic tree of 16 Flaveria species based on RNA-Seq data. The updated phylogeny is largely congruent with the previously published tree but with some modifications. We propose that the data collection method provided in this study can be used as a generic method for phylogenetic tree reconstruction if the target species has no genomic information. We also showed that a “F. pringlei” genotype recently used in a number of labs may be a hybrid between F. pringlei (C3) and F. angustifolia (C3-C4).ConclusionsWe propose that the new strategy of obtaining phylogenetic sequences outlined in this study can be used to construct robust trees in a larger number of taxa. The updated Flaveria phylogenetic tree also supports a hypothesis of stepwise and parallel evolution of C4 photosynthesis in the Flavaria clade.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0399-9) contains supplementary material, which is available to authorized users.

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“…The plant tissue collection will balance tradeoffs between intra-and interspecific diversity (Gemeinholzer et al 2010, Neves andForrest 2011). Tissue from ten individuals of each the species selected for phenology sampling will be collected-from the phenology plot near the tower, Distributed Base Plots (see Thorpe et al 2016), and, when necessary, opportunistically across each site-every five years.…”

Section: Collection Of Materials For Assessments Of Plant Species Genementioning

confidence: 99%

The plant diversity sampling design for The National Ecological Observatory Network

Barnett

Adler

Chemel³

et al. 2019

Ecosphere

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The National Ecological Observatory Network (NEON) is designed to facilitate an understanding of the impact of environmental change on ecological systems. Observations of plant diversity—responsive to changes in climate, disturbance, and land use, and ecologically linked to soil, biogeochemistry, and organisms—result in NEON data products that cross a range of organizational levels. Collections include samples of plant tissue to enable investigations of genetics, plot‐based observations of incidence and cover of native and non‐native species, observations of plant functional traits, archived vouchers of plants, and remote sensing airborne observations. Spatially integrating many ecological observations allows a description of the relationship of plant diversity to climate, land use, organisms, and substrates. Repeating the observations over decades and across the United States will iteratively improve our understanding of those relationships and allow for the testing of system‐level hypotheses as well as the development of predictions of future conditions.

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Plant DNA Sequencing for Phylogenetic Analyses: From Plants to Sequences

Cited by 9 publications

References 90 publications

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications

The plant diversity sampling design for The National Ecological Observatory Network

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