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Catherine Damerval - One of the best experts on this subject based on the ideXlab platform.
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Combining Phylogenetic and Syntenic Analyses for Understanding the Evolution of TCP ECE Genes in
2016Co-Authors: Helene L Citerne, Martine Le Guilloux, Julie Sannier, Sophie Nadot, Catherine DamervalAbstract:TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core Eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core Eudicots, but the evolutionary history of this gene family is unknown in basal Eudicots. Reconstructing the phylogeny of ECE genes in basal Eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal Eudicots and Gunnera which belongs to the sister clade to all other core Eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core Eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse Eudicot lineages may be due to genome-wide duplications. The three major core-Eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanum lycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal Eudicots Aquilegia coerulea an
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combining phylogenetic and syntenic analyses for understanding the evolution of tcp ece genes in Eudicots
PLOS ONE, 2013Co-Authors: Helene L Citerne, Martine Le Guilloux, Julie Sannier, Sophie Nadot, Catherine DamervalAbstract:TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core Eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core Eudicots, but the evolutionary history of this gene family is unknown in basal Eudicots. Reconstructing the phylogeny of ECE genes in basal Eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal Eudicots and Gunnera which belongs to the sister clade to all other core Eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core Eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse Eudicot lineages may be due to genome-wide duplications. The three major core-Eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanum lycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal Eudicots Aquilegia coerulea and Nelumbo nucifera suggests that the two TCP ECE paralogs in these species are also derived from large-scale duplications. TCP ECE loci from basal Eudicots share many features with the three main core Eudicot loci, and allow us to infer the makeup of the ancestral Eudicot locus.
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combining phylogenetic and syntenic analyses for understanding the evolution of tcp ece genes in Eudicots
PLOS ONE, 2013Co-Authors: Helene L Citerne, Martine Le Guilloux, Julie Sannier, Sophie Nadot, Catherine DamervalAbstract:TCP ECE genes encode transcription factors which have received much attention for their repeated recruitment in the control of floral symmetry in core Eudicots, and more recently in monocots. Major duplications of TCP ECE genes have been described in core Eudicots, but the evolutionary history of this gene family is unknown in basal Eudicots. Reconstructing the phylogeny of ECE genes in basal Eudicots will help set a framework for understanding the functional evolution of these genes. TCP ECE genes were sequenced in all major lineages of basal Eudicots and Gunnera which belongs to the sister clade to all other core Eudicots. We show that in these lineages they have a complex evolutionary history with repeated duplications. We estimate the timing of the two major duplications already identified in the core Eudicots within a timeframe before the divergence of Gunnera and after the divergence of Proteales. We also use a synteny-based approach to examine the extent to which the expansion of TCP ECE genes in diverse Eudicot lineages may be due to genome-wide duplications. The three major core-Eudicot specific clades share a number of collinear genes, and their common evolutionary history may have originated at the γ event. Genomic comparisons in Arabidopsis thaliana and Solanum lycopersicum highlight their separate polyploid origin, with syntenic fragments with and without TCP ECE genes showing differential gene loss and genomic rearrangements. Comparison between recently available genomes from two basal Eudicots Aquilegia coerulea and Nelumbo nucifera suggests that the two TCP ECE paralogs in these species are also derived from large-scale duplications. TCP ECE loci from basal Eudicots share many features with the three main core Eudicot loci, and allow us to infer the makeup of the ancestral Eudicot locus.
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Establishment of zygomorphy on an ontogenic spiral and evolution of perianth in the tribe Delphinieae (Ranunculaceae)
Annals of Botany, 2009Co-Authors: Florian Jabbour, Sophie Nadot, Louis P. Ronse De Craene, Catherine DamervalAbstract:† Background and Aims Ranunculaceae presents both ancestral and derived floral traits for Eudicots, and as such is of potential interest to understand key steps involved in the evolution of zygomorphy in Eudicots. Zygomorphy evolved once in Ranunculaceae, in the speciose and derived tribe Delphinieae. This tribe consists of two genera (Aconitum and Delphinium s.l.) comprising more than one-quarter of the species of the family. In this paper, the establishment of zygomorphy during development was investigated to cast light on the origin and evolution of this morphological novelty. † Methods The floral developmental sequence of six species of Ranunculaceae, three actinomorphic (Nigella damascena, Aquilegia alpina and Clematis recta) and three zygomorphic (Aconitum napellus, Delphinium staphisagria and D. grandiflorum), was compared. A developmental model was elaborated to break down the successive acquisitions of floral organ identities on the ontogenic spiral (all the species studied except Aquilegia have a spiral phyllotaxis), giving clues to understanding this complex morphogenesis from an evodevo point of view. In addition, the evolution of symmetry in Ranunculaceae was examined in conjunction with other traits of flowers and with ecological factors. † Key Results In the species studied, zygomorphy is established after organogenesis is completed, and is late, compared with other zygomorphic Eudicot species. Zygomorphy occurs in flowers characterized by a fixed merism and a partially reduced and transformed corolla. † Conclusions It is suggested that shifts in expression of genes controlling the merism, as well as floral symmetry and organ identity, have played a critical role in the evolution of zygomorphy in Delphinieae, while the presence of pollinators able to exploit the peculiar morphology of the flower has been a key factor for the maintenance and diversification of this trait.
Ying Wang - One of the best experts on this subject based on the ideXlab platform.
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functional and evolutionary analysis of the ap1 sep agl6 superclade of mads box genes in the basal Eudicot epimedium sagittatum
Annals of Botany, 2014Co-Authors: Wei Sun, Hongwen Huang, Alice Hayward, Chi Song, Wenjun Huang, Di Liu, Yongliang Liu, Yifei Liu, Ying WangAbstract:† Background and Aims MADS-box transcriptional regulators play important roles during plant development. Based on phylogenetic reconstruction, the AP1/SEP/AGL6 superclade of floral MADS-box genes underwent one or two duplication events in the common ancestor of the core Eudicots. However, the functional evolution of the AP1/ SEP/AGL6 superclade in basal Eudicots remains uncharacterized. Epimedium sagittatum is a basal Eudicot species valued for its medicinal properties and showing unique floral morphology. In this study, structural and functional variation of FUL-like (AP1 subfamily), SEP-like and AGL6-like genes in this species was investigated to further our understanding of flower evolution in angiosperms. Detailed investigations into the microsynteny and evolutionary history of the floral A and E class MADS-box genes in Eudicots were undertaken and used to trace their genomic rearrangements. † Methods One AP1-like gene, two SEP-like genes and one AGL6-like gene were cloned from E. sagittatum .T heir expression patterns were examined using quantitative RT-PCR in different vegetative and reproductive organs at two developmental stages. Yeast two-hybrid assays were carried out among AP1/SEP/AGL6 superclade, AP3/PI and AGAMOUS subfamily members for elucidation of dimerization patterns. In addition, possible formation of a ternary complex involving B class proteins with the A class protein EsFUL-like, the E class SEP-like protein EsAGL2-1 or the AGL6-class protein EsAGL6 were detected using yeast three-hybrid assays. Transgenic Arabidopsis or tobacco plants expressing EsFUL-like, EsAGL2-1 and EsAGL6-like under the cauliflower mosaic virus (CaMV) 35S promoter were generated and analysed. Genomic studies of AP1 syntenic regions in arabidopsis, columbine, strawberry, papaya, peach, grapevine and tomato were conducted for microsyntenic analyses. † Key Results Sequence and phylogenetic analyses showed that EsFUL-like is a member of the AP1 (A class) subfamily, EsAGL2-1 and EsAGL2-2 belong to the SEP-like (E class) subfamily, and EsAGL6-like belongs to the AGL6 (AGL6 class) subfamily. Quantitative RT-PCR analyses revealed that the transcripts of the four genes are absent, or minimal, in vegetative tissues and are most highly expressed in floral organs. Yeast two-hybrid results revealed that of the eight MADS-box proteins tested, only EsAGL6-like, EsAGL2-1 and EsAGL2 were able to form strong homo- and heterodimers, with EsAGL6-like and EsAGL2-1 showing similar interaction patterns. Yeast three-hybrid analysis revealed that EsFUL1-like, EsAGL6-like and EsAGL2-1 (representing the three major lineages of the Epimedium AGL/SEP/ALG6 superclade) could act as bridging proteins in ternary complexes with both EsAP3-2 (B class) and EsPI (B class), which do not heterodimerize themselves. Syntenic analyses of sequenced basal Eudicots, rosids and asterids showed that most AP1-like and SEP-like genes have been tightly associated as neighbours since the origin of basal Eudicots. Ectopic expression of EsFUL-like in arabidopsis caused early flowering through endogenous high-level expression of AP1 and formation of secondary flowers between the first and second whorls. Tobacco plants with ectopic expression of EsAGL2-1 showed shortened pistils and styles, as well as axillary and extra petals in the initial flower. † Conclusions This study provides a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison with a selection of model core Eudicots. The study also highlights how organization in genomic segments containing A and E class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.
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Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal Eudicot Epimedium sagittatum
Annals of Botany, 2014Co-Authors: Wenjun Huang, Zhineng Li, Hongwen Huang, Alice Hayward, Chi Song, Ying WangAbstract:† Background and Aims MADS-box transcriptional regulators play important roles during plant development. Based on phylogenetic reconstruction, the AP1/SEP/AGL6 superclade of floral MADS-box genes underwent one or two duplication events in the common ancestor of the core Eudicots. However, the functional evolution of the AP1/ SEP/AGL6 superclade in basal Eudicots remains uncharacterized. Epimedium sagittatum is a basal Eudicot species valued for its medicinal properties and showing unique floral morphology. In this study, structural and functional variation of FUL-like (AP1 subfamily), SEP-like and AGL6-like genes in this species was investigated to further our understanding of flower evolution in angiosperms. Detailed investigations into the microsynteny and evolutionary history of the floral A and E class MADS-box genes in Eudicots were undertaken and used to trace their genomic rearrangements. † Methods One AP1-like gene, two SEP-like genes and one AGL6-like gene were cloned from E. sagittatum .T heir expression patterns were examined using quantitative RT-PCR in different vegetative and reproductive organs at two developmental stages. Yeast two-hybrid assays were carried out among AP1/SEP/AGL6 superclade, AP3/PI and AGAMOUS subfamily members for elucidation of dimerization patterns. In addition, possible formation of a ternary complex involving B class proteins with the A class protein EsFUL-like, the E class SEP-like protein EsAGL2-1 or the AGL6-class protein EsAGL6 were detected using yeast three-hybrid assays. Transgenic Arabidopsis or tobacco plants expressing EsFUL-like, EsAGL2-1 and EsAGL6-like under the cauliflower mosaic virus (CaMV) 35S promoter were generated and analysed. Genomic studies of AP1 syntenic regions in arabidopsis, columbine, strawberry, papaya, peach, grapevine and tomato were conducted for microsyntenic analyses. † Key Results Sequence and phylogenetic analyses showed that EsFUL-like is a member of the AP1 (A class) subfamily, EsAGL2-1 and EsAGL2-2 belong to the SEP-like (E class) subfamily, and EsAGL6-like belongs to the AGL6 (AGL6 class) subfamily. Quantitative RT-PCR analyses revealed that the transcripts of the four genes are absent, or minimal, in vegetative tissues and are most highly expressed in floral organs. Yeast two-hybrid results revealed that of the eight MADS-box proteins tested, only EsAGL6-like, EsAGL2-1 and EsAGL2 were able to form strong homo- and heterodimers, with EsAGL6-like and EsAGL2-1 showing similar interaction patterns. Yeast three-hybrid analysis revealed that EsFUL1-like, EsAGL6-like and EsAGL2-1 (representing the three major lineages of the Epimedium AGL/SEP/ALG6 superclade) could act as bridging proteins in ternary complexes with both EsAP3-2 (B class) and EsPI (B class), which do not heterodimerize themselves. Syntenic analyses of sequenced basal Eudicots, rosids and asterids showed that most AP1-like and SEP-like genes have been tightly associated as neighbours since the origin of basal Eudicots. Ectopic expression of EsFUL-like in arabidopsis caused early flowering through endogenous high-level expression of AP1 and formation of secondary flowers between the first and second whorls. Tobacco plants with ectopic expression of EsAGL2-1 showed shortened pistils and styles, as well as axillary and extra petals in the initial flower. † Conclusions This study provides a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison with a selection of model core Eudicots. The study also highlights how organization in genomic segments containing A and E class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.
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Characterization of a Crabs Claw Gene in Basal Eudicot Species Epimedium sagittatum (Berberidaceae)
International Journal of Molecular Sciences, 2013Co-Authors: Wenjun Huang, Zhineng Li, Haiyan Lv, Hongwen Huang, Ying WangAbstract:The Crabs Claw (CRC) YABBY gene is required for regulating carpel development in angiosperms and has played an important role in nectary evolution during core Eudicot speciation. The function or expression of CRC-like genes has been explored in two basal Eudicots, Eschscholzia californica and Aquilegia formosa. To further investigate the function of CRC orthologous genes related to evolution of carpel and nectary development in basal Eudicots, a CRC ortholog, EsCRC, was isolated and characterized from Epimedium sagittatum (Sieb. and Zucc.) Maxim. A phylogenetic analysis of EsCRC and previously identified CRC-like genes placed EsCRC within the basal Eudicot lineage. Gene expression results suggest that EsCRC is involved in the development of sepals and carpels, but not nectaries. Phenotypic complementation of the Arabidopsis mutant crc-1 was achieved by constitutive expression of EsCRC. In addition, over-expression of EsCRC in Arabidopsis and tobacco gave rise to abaxially curled leaves. Transgenic results together with the gene expression analysis suggest that EsCRC may maintain a conserved function in carpel development and also play a novel role related to sepal formation. Absence of EsCRC and ElCRC expression in nectaries further indicates that nectary development in non-core Eudicots is unrelated to expression of CRC-like genes.
Kent E Holsinger - One of the best experts on this subject based on the ideXlab platform.
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s rnase mediated gametophytic self incompatibility is ancestral in Eudicots
Molecular Biology and Evolution, 2002Co-Authors: J E Steinbachs, Kent E HolsingerAbstract:: The evolutionary relationship between self-incompatibility systems in different families of flowering plants has long been a topic of interest. Physiological differences in the mode of gene action and the enormous sequence differences between genes with different modes of action suggest that many instances of self-incompatibility have arisen independently. In contrast, previous analyses of the S-RNase associated with gametophytic self-incompatibility in the Eudicot families (Solanaceae, Scrophulariaceae, and Rosaceae) have suggested that sequences within families form well-supported and distinct lineages. In this study we demonstrate that in fact, S-RNase-mediated gametophytic self-incompatibility evolved only once in the Eudicots.
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S-RNase–mediated Gametophytic Self-Incompatibility is Ancestral in Eudicots
Molecular Biology and Evolution, 2002Co-Authors: J E Steinbachs, Kent E HolsingerAbstract:: The evolutionary relationship between self-incompatibility systems in different families of flowering plants has long been a topic of interest. Physiological differences in the mode of gene action and the enormous sequence differences between genes with different modes of action suggest that many instances of self-incompatibility have arisen independently. In contrast, previous analyses of the S-RNase associated with gametophytic self-incompatibility in the Eudicot families (Solanaceae, Scrophulariaceae, and Rosaceae) have suggested that sequences within families form well-supported and distinct lineages. In this study we demonstrate that in fact, S-RNase-mediated gametophytic self-incompatibility evolved only once in the Eudicots.
Zhineng Li - One of the best experts on this subject based on the ideXlab platform.
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Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal Eudicot Epimedium sagittatum
Annals of Botany, 2014Co-Authors: Wenjun Huang, Zhineng Li, Hongwen Huang, Alice Hayward, Chi Song, Ying WangAbstract:† Background and Aims MADS-box transcriptional regulators play important roles during plant development. Based on phylogenetic reconstruction, the AP1/SEP/AGL6 superclade of floral MADS-box genes underwent one or two duplication events in the common ancestor of the core Eudicots. However, the functional evolution of the AP1/ SEP/AGL6 superclade in basal Eudicots remains uncharacterized. Epimedium sagittatum is a basal Eudicot species valued for its medicinal properties and showing unique floral morphology. In this study, structural and functional variation of FUL-like (AP1 subfamily), SEP-like and AGL6-like genes in this species was investigated to further our understanding of flower evolution in angiosperms. Detailed investigations into the microsynteny and evolutionary history of the floral A and E class MADS-box genes in Eudicots were undertaken and used to trace their genomic rearrangements. † Methods One AP1-like gene, two SEP-like genes and one AGL6-like gene were cloned from E. sagittatum .T heir expression patterns were examined using quantitative RT-PCR in different vegetative and reproductive organs at two developmental stages. Yeast two-hybrid assays were carried out among AP1/SEP/AGL6 superclade, AP3/PI and AGAMOUS subfamily members for elucidation of dimerization patterns. In addition, possible formation of a ternary complex involving B class proteins with the A class protein EsFUL-like, the E class SEP-like protein EsAGL2-1 or the AGL6-class protein EsAGL6 were detected using yeast three-hybrid assays. Transgenic Arabidopsis or tobacco plants expressing EsFUL-like, EsAGL2-1 and EsAGL6-like under the cauliflower mosaic virus (CaMV) 35S promoter were generated and analysed. Genomic studies of AP1 syntenic regions in arabidopsis, columbine, strawberry, papaya, peach, grapevine and tomato were conducted for microsyntenic analyses. † Key Results Sequence and phylogenetic analyses showed that EsFUL-like is a member of the AP1 (A class) subfamily, EsAGL2-1 and EsAGL2-2 belong to the SEP-like (E class) subfamily, and EsAGL6-like belongs to the AGL6 (AGL6 class) subfamily. Quantitative RT-PCR analyses revealed that the transcripts of the four genes are absent, or minimal, in vegetative tissues and are most highly expressed in floral organs. Yeast two-hybrid results revealed that of the eight MADS-box proteins tested, only EsAGL6-like, EsAGL2-1 and EsAGL2 were able to form strong homo- and heterodimers, with EsAGL6-like and EsAGL2-1 showing similar interaction patterns. Yeast three-hybrid analysis revealed that EsFUL1-like, EsAGL6-like and EsAGL2-1 (representing the three major lineages of the Epimedium AGL/SEP/ALG6 superclade) could act as bridging proteins in ternary complexes with both EsAP3-2 (B class) and EsPI (B class), which do not heterodimerize themselves. Syntenic analyses of sequenced basal Eudicots, rosids and asterids showed that most AP1-like and SEP-like genes have been tightly associated as neighbours since the origin of basal Eudicots. Ectopic expression of EsFUL-like in arabidopsis caused early flowering through endogenous high-level expression of AP1 and formation of secondary flowers between the first and second whorls. Tobacco plants with ectopic expression of EsAGL2-1 showed shortened pistils and styles, as well as axillary and extra petals in the initial flower. † Conclusions This study provides a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison with a selection of model core Eudicots. The study also highlights how organization in genomic segments containing A and E class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.
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Isolation and functional analyses of a putative floral homeotic C-function gene in a basal Eudicot London plane tree (Platanus acerifolia).
PLOS ONE, 2013Co-Authors: Jiaqi Zhang, Zhineng LiAbstract:The identification of mutants in model plant species has led to the isolation of the floral homeotic function genes that play crucial roles in flower organ specification. However, floral homeotic C-function genes are rarely studied in basal Eudicots. Here, we report the isolation and characterization of the AGAMOUS (AG) orthologous gene (PaAG) from a basal Eudicot London plane tree (Platanus acerifolia Willd). Phylogenetic analysis showed that PaAG belongs to the C- clade AG group of genes. PaAG was found to be expressed predominantly in the later developmental stages of male and female inflorescences. Ectopic expression of PaAG-1 in tobacco (Nicotiana tabacum) resulted in morphological alterations of the outer two flower whorls, as well as some defects in vegetative growth. Scanning electron micrographs (SEMs) confirmed homeotic sepal-to-carpel transformation in the transgenic plants. Protein interaction assays in yeast cells indicated that PaAG could interact directly with PaAP3 (a B-class MADS-box protein in P. acerifolia), and also PaSEP1 and PaSEP3 (E-class MADS-box proteins in P. acerifolia). This study performed the functional analysis of AG orthologous genes outside core Eudicots and monocots. Our findings demonstrate a conserved functional role of AG homolog in London plane tree, which also represent a contribution towards understanding the molecular mechanisms of flower development in this monoecious tree species.
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Characterization of a Crabs Claw Gene in Basal Eudicot Species Epimedium sagittatum (Berberidaceae)
International Journal of Molecular Sciences, 2013Co-Authors: Wenjun Huang, Zhineng Li, Haiyan Lv, Hongwen Huang, Ying WangAbstract:The Crabs Claw (CRC) YABBY gene is required for regulating carpel development in angiosperms and has played an important role in nectary evolution during core Eudicot speciation. The function or expression of CRC-like genes has been explored in two basal Eudicots, Eschscholzia californica and Aquilegia formosa. To further investigate the function of CRC orthologous genes related to evolution of carpel and nectary development in basal Eudicots, a CRC ortholog, EsCRC, was isolated and characterized from Epimedium sagittatum (Sieb. and Zucc.) Maxim. A phylogenetic analysis of EsCRC and previously identified CRC-like genes placed EsCRC within the basal Eudicot lineage. Gene expression results suggest that EsCRC is involved in the development of sepals and carpels, but not nectaries. Phenotypic complementation of the Arabidopsis mutant crc-1 was achieved by constitutive expression of EsCRC. In addition, over-expression of EsCRC in Arabidopsis and tobacco gave rise to abaxially curled leaves. Transgenic results together with the gene expression analysis suggest that EsCRC may maintain a conserved function in carpel development and also play a novel role related to sepal formation. Absence of EsCRC and ElCRC expression in nectaries further indicates that nectary development in non-core Eudicots is unrelated to expression of CRC-like genes.
Hengchang Wang - One of the best experts on this subject based on the ideXlab platform.
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complete plastome sequencing of both living species of circaeasteraceae ranunculales reveals unusual rearrangements and the loss of the ndh gene family
BMC Genomics, 2017Co-Authors: Yanxia Sun, Aiping Meng, Michael J. Moore, Nan Lin, Kole Adelalu, Shuguang Jian, Linsen Yang, Hengchang WangAbstract:Among the 13 families of early-diverging Eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent Eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging Eudicots and to further investigate the phylogenetic position of Circaeasteraceae. Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and . Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging Eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging Eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging Eudicots and to better understand relationships within Ranunculales .
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Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family
BMC, 2017Co-Authors: Yanxia Sun, Aiping Meng, Michael J. Moore, Nan Lin, Kole Adelalu, Shuguang Jian, Linsen Yang, Hengchang WangAbstract:Abstract Background Among the 13 families of early-diverging Eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent Eudicots. Hence it is important to sequence plastomes from Circaeasteraceae to better understand plastome evolution in early-diverging Eudicots and to further investigate the phylogenetic position of Circaeasteraceae. Results Using an Illumina HiSeq 2000, complete plastomes were sequenced from both living members of Circaeasteraceae: Circaeaster agrestis and Kingdonia uniflora . Plastome structure and gene content were compared between these two plastomes, and with those of other early-diverging Eudicot plastomes. Phylogenetic analysis of a 79-gene, 99-taxon data set including exemplars of all families of early-diverging Eudicots was conducted to resolve the phylogenetic position of Circaeasteraceae. Both plastomes possess the typical quadripartite structure of land plant plastomes. However, a large ~49 kb inversion and a small ~3.5 kb inversion were found in the large single-copy regions of both plastomes, while Circaeaster possesses a number of other rearrangements, particularly in the Inverted Repeat. In addition, infA was found to be a pseudogene and accD was found to be absent within Circaeaster, whereas all ndh genes, except for ndhE and ndhJ, were found to be either pseudogenized (ΨndhA, ΨndhB, ΨndhD, ΨndhH and ΨndhK) or absent (ndhC, ndhF, ndhI and ndhG) in Kingdonia. Circaeasteraceae was strongly supported as sister to Lardizabalaceae in phylogenetic analyses. Conclusion The first plastome sequencing of Circaeasteraceae resulted in the discovery of several unusual rearrangements and the loss of ndh genes, and confirms the sister relationship between Circaeasteraceae and Lardizabalaceae. This research provides new insight to characterize plastome structural evolution in early-diverging Eudicots and to better understand relationships within Ranunculales
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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, Aiping Meng, Xiaodong Li, Pamela S. Soltis, Douglas E. Soltis, Tingting Zhao, Shoujun Zhang, 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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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, Aiping Meng, Xiaodong Li, Pamela S. Soltis, Douglas E. Soltis, Tingting Zhao, Shoujun Zhang, 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, Aiping Meng, Pamela S. Soltis, Douglas E. Soltis, 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.