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Caio Guilherme Pereira - One of the best experts on this subject based on the ideXlab platform.
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Eudicots from severely phosphorus impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
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Eudicots from severely phosphorus‐impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
Hans Lambers - One of the best experts on this subject based on the ideXlab platform.
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Eudicots from severely phosphorus impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
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Eudicots from severely phosphorus‐impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
Douglas E. Soltis - One of the best experts on this subject based on the ideXlab platform.
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Evolution of genome size in the angiosperms.
American Journal of Botany, 2020Co-Authors: Douglas E. Soltis, Michael D. Bennett, Pamela S Soltis, Ilia J. LeitchAbstract:Genome size varies extensively across the flowering plants, which has stimulated speculation regarding the ancestral genome size of these plants and trends in genome evolution. We investigated the evolution of C-values across the angiosperms using a molecular phylogenetic framework and C-values not previously available for crucial basal angiosperms, including Amborella, Illiciaceae, and Austrobaileya. Reconstructions of genome size across the angiosperms and extant gymnosperms indicate that the ancestral genome size for angiosperms is very small (1C # 1.4 pg), in agreement with an earlier analysis of Leitch et al. (1998). Furthermore, a very small genome size (1C # 1.4 pg) is ancestral not only for the angiosperms in general, but also for most major clades of flowering plants, including the monocots and the Eudicots. The ancestral genome of core Eudicots may also have been very small given that very low 1C-values appear to be ancestral for major clades of core Eudicots, such as Caryophyllales, Saxifragales, and asterids. Very large genomes occur in clades that occupy derived positions within the monocots and Santalales.
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The origin and diversification of angiosperms.
American Journal of Botany, 2020Co-Authors: Pamela S Soltis, Douglas E. SoltisAbstract:The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of Eudicots include Ranunculales, which are sister to all other Eudicots, and a Glade of core Eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and Eudicots, (2) branching order among basal Eudicots, (3) relationships among the major clades of core Eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.
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phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early diverging Eudicots including an angiosperm wide analysis of ir gene content evolution
Molecular Phylogenetics and Evolution, 2016Co-Authors: Michael J Moore, Pamela S Soltis, Douglas E. Soltis, Shoujun Zhang, Tingting Zhao, Aiping Meng, Xiaodong Li, Jianqiang Li, Hengchang WangAbstract:Abstract The grade of early-diverging Eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging Eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging Eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging Eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of Eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging Eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses.
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complete plastid genome sequencing of trochodendraceae reveals a significant expansion of the inverted repeat and suggests a paleogene divergence between the two extant species
PLOS ONE, 2013Co-Authors: Michael J Moore, Pamela S Soltis, Douglas E. Soltis, Aiping Meng, Jianqiang Li, Hengchang WangAbstract:The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core Eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.
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living stones reveal alternative petal identity programs within the core Eudicots
Plant Journal, 2012Co-Authors: Pamela S Soltis, Paula J Rudall, Samuel F Brockington, Michael W Frohlich, David G Oppenheimer, Douglas E. SoltisAbstract:*SUMMARY Petals, defined as the showy laminar floral organs in the second floral whorl, have been shown to be under similar genetic control in distantly related core eudicot model organisms. On the basis of these findings, it is commonly assumed that the petal identity program regulated by B-class MADS-box gene homologs is invariant across the core eudicot clade. However, the core Eudicots, which comprise >70% of angiosperm species, exhibit numerous instances of petal and sepal loss, transference of petal function between floral whorls, and recurrent petal evolution. In the face of these complex patterns of perianth evolution, the concept of a core eudicot petal identity program has not been tested. We therefore examined the petal identity program in the Caryophyllales, a core eudicot clade in which perianth differentiation into sepals and petals has evolved multiple times. Specifically, we analyzed the expression patterns of B- and C-class MADS-box homologs for evidence of a conserved petal identity program between sepal-derived and stamen-derived petaloid organs in the ‘living stone’ family Aizoaceae. We found that neither sepal-derived nor stamen-derived petaloid organs exhibit gene expression patterns consistent with the core eudicot petal identity program. B-class gene homologs are not expressed during the development of sepal-derived petals and are not implicated in petal identity in stamenderived petals, as their transient expression coincides with early expression of the C-class homolog. We therefore provide evidence for petal development that is independent of B-class genes and suggest that different genetic control of petal identity has evolved within this lineage of core Eudicots. These findings call for a more comprehensive understanding of perianth variation and its genetic causes within the core Eudicots – an endeavor that will have broader implications for the interpretation of perianth evolution across angiosperms.
Rafael S Oliveira - One of the best experts on this subject based on the ideXlab platform.
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Eudicots from severely phosphorus impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
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Eudicots from severely phosphorus‐impoverished environments preferentially allocate phosphorus to their mesophyll
New Phytologist, 2018Co-Authors: Caio Guilherme Pereira, Peta L Clode, Rafael S Oliveira, Hans LambersAbstract:: Plants allocate nutrients to specific leaf cell types, with commelinoid monocots preferentially allocating phosphorus (P) to the mesophyll and calcium (Ca) to the epidermis, whereas the opposite is thought to occur in Eudicots. However, Proteaceae from severely P-impoverished habitats present the same P-allocation pattern as monocots. This raises the question of whether preferential P allocation to mesophyll cells is a phylogenetically conserved trait, exclusive to commelinoid monocots and a few Proteaceae, or a trait that has evolved multiple times to allow plants to cope with very low soil P availability. We analysed the P-allocation patterns of 16 species from 10 genera, eight families and six orders within three major clades of Eudicots across different P-impoverished environments in Australia and Brazil, using elemental X-ray mapping to quantitatively determine leaf cell-specific nutrient concentrations. Many of the analysed species showed P-allocation patterns that differed substantially from that expected for Eudicots. Instead, P-allocation patterns were strongly associated with the P availability in the natural habitat of the species, suggesting a convergent evolution of P-allocation patterns at the cellular level, with P limitation as selective pressure and without a consistent P-allocation pattern within Eudicots. Here, we show that most Eudicots from severely P-impoverished environments preferentially allocated P to their mesophyll. We surmise that this preferential P allocation to photosynthetically active cells might contribute to the very high photosynthetic P-use efficiency of species adapted to P-impoverished habitats.
Pamela S Soltis - One of the best experts on this subject based on the ideXlab platform.
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Evolution of genome size in the angiosperms.
American Journal of Botany, 2020Co-Authors: Douglas E. Soltis, Michael D. Bennett, Pamela S Soltis, Ilia J. LeitchAbstract:Genome size varies extensively across the flowering plants, which has stimulated speculation regarding the ancestral genome size of these plants and trends in genome evolution. We investigated the evolution of C-values across the angiosperms using a molecular phylogenetic framework and C-values not previously available for crucial basal angiosperms, including Amborella, Illiciaceae, and Austrobaileya. Reconstructions of genome size across the angiosperms and extant gymnosperms indicate that the ancestral genome size for angiosperms is very small (1C # 1.4 pg), in agreement with an earlier analysis of Leitch et al. (1998). Furthermore, a very small genome size (1C # 1.4 pg) is ancestral not only for the angiosperms in general, but also for most major clades of flowering plants, including the monocots and the Eudicots. The ancestral genome of core Eudicots may also have been very small given that very low 1C-values appear to be ancestral for major clades of core Eudicots, such as Caryophyllales, Saxifragales, and asterids. Very large genomes occur in clades that occupy derived positions within the monocots and Santalales.
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The origin and diversification of angiosperms.
American Journal of Botany, 2020Co-Authors: Pamela S Soltis, Douglas E. SoltisAbstract:The angiosperms, one of five groups of extant seed plants, are the largest group of land plants. Despite their relatively recent origin, this clade is extremely diverse morphologically and ecologically. However, angiosperms are clearly united by several synapomorphies. During the past 10 years, higher-level relationships of the angiosperms have been resolved. For example, most analyses are consistent in identifying Amborella, Nymphaeaceae, and Austrobaileyales as the basalmost branches of the angiosperm tree. Other basal lineages include Chloranthaceae, magnoliids, and monocots. Approximately three quarters of all angiosperm species belong to the eudicot clade, which is strongly supported by molecular data but united morphologically by a single synapomorphy-triaperturate pollen. Major clades of Eudicots include Ranunculales, which are sister to all other Eudicots, and a Glade of core Eudicots, the largest members of which are Saxifragales, Caryophyllales, rosids, and asterids. Despite rapid progress in resolving angiosperm relationships, several significant problems remain: (1) relationships among the monocots, Chloranthaceae, magnoliids, and Eudicots, (2) branching order among basal Eudicots, (3) relationships among the major clades of core Eudicots, (4) relationships within rosids, (5) relationships of the many lineages of parasitic plants, and (6) integration of fossils with extant taxa into a comprehensive tree of angiosperm phylogeny.
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phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early diverging Eudicots including an angiosperm wide analysis of ir gene content evolution
Molecular Phylogenetics and Evolution, 2016Co-Authors: Michael J Moore, Pamela S Soltis, Douglas E. Soltis, Shoujun Zhang, Tingting Zhao, Aiping Meng, Xiaodong Li, Jianqiang Li, Hengchang WangAbstract:Abstract The grade of early-diverging Eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging Eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging Eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging Eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of Eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging Eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses.
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complete plastid genome sequencing of trochodendraceae reveals a significant expansion of the inverted repeat and suggests a paleogene divergence between the two extant species
PLOS ONE, 2013Co-Authors: Michael J Moore, Pamela S Soltis, Douglas E. Soltis, Aiping Meng, Jianqiang Li, Hengchang WangAbstract:The early-diverging eudicot order Trochodendrales contains only two monospecific genera, Tetracentron and Trochodendron. Although an extensive fossil record indicates that the clade is perhaps 100 million years old and was widespread throughout the Northern Hemisphere during the Paleogene and Neogene, the two extant genera are both narrowly distributed in eastern Asia. Recent phylogenetic analyses strongly support a clade of Trochodendrales, Buxales, and Gunneridae (core Eudicots), but complete plastome analyses do not resolve the relationships among these groups with strong support. However, plastid phylogenomic analyses have not included data for Tetracentron. To better resolve basal eudicot relationships and to clarify when the two extant genera of Trochodendrales diverged, we sequenced the complete plastid genome of Tetracentron sinense using Illumina technology. The Tetracentron and Trochodendron plastomes possess the typical gene content and arrangement that characterize most angiosperm plastid genomes, but both genomes have the same unusual ∼4 kb expansion of the inverted repeat region to include five genes (rpl22, rps3, rpl16, rpl14, and rps8) that are normally found in the large single-copy region. Maximum likelihood analyses of an 83-gene, 88 taxon angiosperm data set yield an identical tree topology as previous plastid-based trees, and moderately support the sister relationship between Buxaceae and Gunneridae. Molecular dating analyses suggest that Tetracentron and Trochodendron diverged between 44-30 million years ago, which is congruent with the fossil record of Trochodendrales and with previous estimates of the divergence time of these two taxa. We also characterize 154 simple sequence repeat loci from the Tetracentron sinense and Trochodendron aralioides plastomes that will be useful in future studies of population genetic structure for these relict species, both of which are of conservation concern.
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a targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
Applications in Plant Sciences, 2013Co-Authors: Samuel F Brockington, Michael J Moore, Gregory W Stull, Venkata S Mandala, Norman A Douglas, Heatherrose Kates, Xinshuai Qi, Pamela S SoltisAbstract:Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms. Methods and Results: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization-based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 Eudicots, two monocots), which were subsequently sequenced on a single lane of the Illumina GAIIx with single-end, 100-bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717×), even for the two monocots. Conclusions: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvement...