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Yanxia Sun - One of the best experts on this subject based on the ideXlab platform.
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genomic insights into adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
New Phytologist, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong ZhangAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
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genome sequencing of the endangered kingdonia uniflora circaeasteraceae Ranunculales reveals potential mechanisms of evolutionary specialization
iScience, 2020Co-Authors: Yanxia Sun, Nan Lin, Michael J Moore, Xu Zhang, Jacob B Landis, Huajie Zhang, Tao Deng, Aidi Zhang, Jinling HuangAbstract:Summary Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.
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genome wide sequencing provides evidence of adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
bioRxiv, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong Zhang, Tao DengAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome‐environment association analyses identified 16 putatively adaptive loci related to biotic and abiotic stress resistance. Our genome wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing conservation efforts.
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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, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Michael J Moore, 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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Additional file 6: of Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family
2017Co-Authors: Yanxia Sun, Michael Moore, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Hengchang WangAbstract:Repeats âĽ30 bp in the plastomes of seven other Ranunculales species. (DOC 30 kb
Yi Ren - One of the best experts on this subject based on the ideXlab platform.
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heterodichogamy in kingdonia circaeasteraceae Ranunculales
Annals of Botany, 2012Co-Authors: Yi Ren, Liang Zhao, Xumei Wang, Peng Zhang, Peter K. EndressAbstract:† Background and Aims Preliminary field observations in 2001 and 2002 suggested that Kingdonia uniflora (Circaeasteraceae, Ranunculales) exhibits heterodichogamy, an unusual kind of reproductive heteromorphy, hitherto unreported in Ranunculales and known from only one other genus in basal eudicots. † Methods During several subsequent years flowers were observed in the field. Flowers were fixed in FAA and studied with microtome sections series and with the scanning electron microscope. † Key Results The flowers proved to be heterodichogamous, with protandrous and protogynous morphs, which have a 1 : 1 ratio. Both morphs equally set fruit. Each year a single flower is formed at the tip of a rhizome or more rarely two flowers. The flowers are already open when they appear at the soil surface, before they are receptive and before pollen is dispersed. In both floral morphs the styles elongate early and the stigmas are positioned above the anthers before anthesis begins. In protogynous flowers the stigmas become receptive in this position; later the styles become reflexed and then the anthers dehisce. In contrast, in protandrous flowers the stamen filaments elongate during early anthesis such that the dehiscing anthers come to lie above the (still unreceptive) stigmas; after dehiscence of all anthers in a flower the styles begin to elongate and become receptive. † Conclusions This is the first record of heterodichogamy in a representative of Ranunculales, in an herbaceous eudicot, and in a plant with uniflorous ramets. The occurrence of heterodichogamy in Kingdonia in which clonal reproduction appears to be dominant might be an adaptation to avoid mating between the ramets from a common mother individual (genet).
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comparative floral development in lardizabalaceae Ranunculales
Botanical Journal of the Linnean Society, 2011Co-Authors: Xiaohui Zhang, Yi RenAbstract:Lardizabalaceae, one of seven families of Ranunculales, represent a monophyletic group. The family has functionally unisexual flowers with the organs in trimerous whorls, petaloid sepals and sometimes nectariferous petals. Among Ranunculales, Lardizabalaceae share several floral characters and climbing habit with Menispermaceae, but molecular analyses indicate that Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Morphological and ontogenetic studies of flowers have proved to be a good complement to molecular data in clarifying relationships. Floral organogenesis has been studied in very few species of the family. This study investigates the comparative floral development of three species from three genera (Decaisnea, Akebia and Holboellia) of Lardizabalaceae using scanning electron microscopy. Flowers have a whorled phyllotaxis. Within each whorl, the organs are initiated either simultaneously or in a rapid spiral sequence. In Akebia, six sepals are initiated, but one to three sepals of the second whorl do not further develop. The presence of three sepals in Akebia is thus a developmentally secondary simplification. The petals (if present) are retarded in early developmental stages; stamens and petals are different in shape from the beginning of development. The retarded petals may not be derived from staminodes in Lardizabalaceae. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 166, 171–184.
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phylogeny and classification of Ranunculales evidence from four molecular loci and morphological data
Perspectives in Plant Ecology Evolution and Systematics, 2009Co-Authors: Wei Wang, Yi Ren, Mary E Endress, Zhiduan ChenAbstract:Previous phylogenetic analyses of Ranunculales, which have mostly been focused on an individual family and were based on molecular data alone, have recovered three main clades within the order. However, support for relationships among these three clades was weak. Earlier hypotheses were often hampered by limited taxon sampling; to date less than one-tenth of the genera in the order have been sampled. In this study, we used a greatly enlarged taxon sampling (105 species, representing 99 genera of all seven families in the order). Our study is, furthermore, the first to employ morphology (65 characters) in combination with sequence data from four genomic regions, including plastid rbcL, matK and trnL-F, and nuclear ribosomal 26S rDNA to reconstruct phylogenetic relationships within Ranunculales. Maximum parsimony and Bayesian inference were performed on the individual and combined data sets. Our analyses concur with those of previous studies, but in most cases provide stronger support and better resolution for relationships among the three main clades retrieved. The first, comprised solely of the monogeneric family Eupteleaceae, is the earliest-diverging lineage. The second clade is composed exclusively of taxa of Papaveraceae, which is sister to the third clade, the core Ranunculales, comprising the other five families of the order. Circaeasteraceae and Lardizabalaceae form a strongly supported clade. Pteridophyllum is supported as sister to Hypecoum, contradicting the viewpoint that the former is the earliest-diverging genus in Papaveraceae. Glaucidium is basalmost in Ranunculaceae. Within this phylogenetic framework, the evolution of selected characters is inferred and diagnostic morphological characters at different taxonomic levels are identified and discussed. Based on both morphological and molecular evidence, a classification outline for Ranunculales is presented, including the proposal of two new subfamilies, Menispermoideae and Tinosporoideae in Menispermaceae and a new tribe, Callianthemeae, for the genus Callianthemum (Ranunculaceae).
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floral morphogenesis in euptelea eupteleaceae Ranunculales
Annals of Botany, 2007Co-Authors: Yi Ren, Liang Zhao, Peter K. EndressAbstract:† Background and Aims Based on molecular phylogenetic studies, the unigeneric family Eupteleaceae has a prominent phylogenetic position at or near the base of Ranunculales, which, in turn, appear at the base of eudicots. The aim of the present paper is to reveal developmental features of the flowers and to put the genus in a morphological context with other basal eudicots. † Methods Flowers in all developmental stages of Euptelea pleiosperma were collected in the wild at intervals of 7‐10 d in the critical stages and studied with a scanning electron microscope. † Key Results Remnants of a perianth are lacking throughout flower development. Floral symmetry changes from monosymmetric to asymmetric to disymmetric during development. Asymmetry is expressed in that the sequence of stamen initiation is from the centre to both lateral sides on the adaxial side of the flower but starting from one lateral side and proceeding to the other on the abaxial side. Despite the pronounced floral disymmetry, a dimerous pattern of floral organs was not found. The carpel primordia arise between the already large stamens and alternate with them. Stamens and carpels each form a somewhat irregular whorl. The carpels are ascidiate from the beginning. The stigma differentiates as two crests along the ventral slit of the ovary. The few lateral ovules alternate with each other. † Conclusions Although the flowers have some unusual autapomorphies (wind pollination, lack of a perianth, pronounced disymmetry of the floral base, long connective protrusion, long temporal gap between androecium and gynoecium initiation, small space for carpel initiation), they show some plesiomorphies at the level of basal eudicots (free carpels, basifixed anthers, whorled phyllotaxis), and thus fit well in Ranunculales.
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development of flowers and inflorescences of circaeaster circaeasteraceae Ranunculales
Plant Systematics and Evolution, 2005Co-Authors: Xianhua Tian, L Zhang, Yi RenAbstract:The flower organs of Circaeaster are spiral in origin. The primordia of the tepals, stamens and carpels are almost the same in shape and size in early development. Carpel conduplication takes place only in the middle part of the carpel. The basal part of the carpel differentiates into a short stalk and the upper part into the style and the stigma. Flower development is similar to that of Kingdonia. Floral development of Circaeaster is compared with that of other Ranunculales.
Elena M Kramer - One of the best experts on this subject based on the ideXlab platform.
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Homologs of the STYLISH gene family control nectary development in Aquilegia.
New Phytologist, 2018Co-Authors: Ya Min, J. Imani Bunn, Elena M KramerAbstract:Floral nectaries are an interesting example of a convergent trait in flowering plants, and are associated with the diversification of numerous angiosperm lineages, including the adaptive radiation of the New World Aquilegia species. However, we know very little as to what genes contribute to nectary development and evolution, particularly in noncore eudicot taxa. We analyzed expression patterns and used RNAi-based methods to investigate the functions of homologs from the STYLISH (STY) family in nectar spur development in Aquilegia coerulea. We found that AqSTY1 exhibits concentrated expression in the presumptive nectary of the growing spur tip, and triple gene silencing of the three STY-like genes revealed that they function in style and nectary development. Strong expression of STY homologs was also detected in the nectary-bearing petals of Delphinium and Epimedium. Our results suggest that the novel recruitment of STY homologs to control nectary development is likely to have occurred before the diversification of the Ranunculaceae and Berberidaceae. To date, the STY homologs of the Ranunculales are the only alternative loci for the control of nectary development in flowering plants, providing a critical data point in understanding the evolutionary origin and developmental basis of nectaries.
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Aquilegia B gene homologs promote petaloidy of the sepals and maintenance of the C domain boundary.
EvoDevo, 2017Co-Authors: Bharti Sharma, Elena M KramerAbstract:The model Aquilegia coerulea x "Origami" possesses several interesting floral features, including petaloid sepals that are morphologically distinct from the true petals and a broad domain containing many whorls of stamens. We undertook the current study in an effort to understand the former trait, but additionally uncovered data that inform on the latter. The Aquilegia B gene homolog AqPI is shown to contribute to the production of anthocyanin in the first whorl sepals, although it has no major role in their morphology. Surprisingly, knockdown of AqPI in Aquilegia coerulea x "Origami" also reveals a role for the B class genes in maintaining the expression of the C gene homolog AqAG1 in the outer whorls of stamens. These findings suggest that the transference of pollinator function to the first whorl sepals included a non-homeotic recruitment of the B class genes to promote aspects of petaloidy. They also confirm results in several other Ranunculales that have revealed an unexpected regulatory connection between the B and C class genes.
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petal specific subfunctionalization of an apetala3 paralog in the Ranunculales and its implications for petal evolution
New Phytologist, 2011Co-Authors: Bharti Sharma, Hongzhi Kong, Elena M KramerAbstract:Summary • The petals of the lower eudicot family Ranunculaceae are thought to have been derived many times independently from stamens. However, investigation of the genetic basis of their identity has suggested an alternative hypothesis: that they share a commonly inherited petal identity program. This theory is based on the fact that an ancient paralogous lineage of APETALA3 (AP3) in the Ranunculaceae appears to have a conserved, petal-specific expression pattern. • Here, we have used a combination of approaches, including RNAi, comparative gene expression and molecular evolutionary studies, to understand the function of this petal-specific AP3 lineage. • Functional analysis of the Aquilegia locus AqAP3-3 has demonstrated that the paralog is required for petal identity with little contribution to the identity of the other floral organs. Expanded expression studies and analyses of molecular evolutionary patterns provide further evidence that orthologs of AqAP3-3 are primarily expressed in petals and are under higher purifying selection across the family than the other AP3 paralogs. • Taken together, these findings suggest that the AqAP3-3 lineage underwent progressive subfunctionalization within the order Ranunculales, ultimately yielding a specific role in petal identity that has probably been conserved, in stark contrast with the multiple independent origins predicted by botanical theories.
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one size fits all molecular evidence for a commonly inherited petal identity program in Ranunculales
American Journal of Botany, 2009Co-Authors: David A Rasmussen, Elena M Kramer, Elizabeth A ZimmerAbstract:Petaloid organs are a major component of the floral diversity observed across nearly all major clades of angiosperms. The variable morphology and development of these organs has led to the hypothesis that they are not homologous but, rather, have evolved multiple times. A particularly notable example of petal diversity, and potential homoplasy, is found within the order Ranunculales, exemplified by families such as Ranunculaceae, Berberidaceae, and Papaveraceae. To investigate the molecular basis of petal identity in Ranunculales, we used a combination of molecular phylogenetics and gene expression analysis to characterize APETALA3 (AP3) and PISTILLATA (PI) homologs from a total of 13 representative genera of the order. One of the most striking results of this study is that expression of orthologs of a single AP3 lineage is consistently petal-specific across both Ranunculaceae and Berberidaceae. We conclude from this finding that these supposedly homoplastic petals in fact share a developmental genetic program that appears to have been present in the common ancestor of the two families. We discuss the implications of this type of molecular data for long-held typological definitions of petals and, more broadly, the evolution of petaloid organs across the angiosperms.
Nan Lin - One of the best experts on this subject based on the ideXlab platform.
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genomic insights into adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
New Phytologist, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong ZhangAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
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genome sequencing of the endangered kingdonia uniflora circaeasteraceae Ranunculales reveals potential mechanisms of evolutionary specialization
iScience, 2020Co-Authors: Yanxia Sun, Nan Lin, Michael J Moore, Xu Zhang, Jacob B Landis, Huajie Zhang, Tao Deng, Aidi Zhang, Jinling HuangAbstract:Summary Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.
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genome wide sequencing provides evidence of adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
bioRxiv, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong Zhang, Tao DengAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome‐environment association analyses identified 16 putatively adaptive loci related to biotic and abiotic stress resistance. Our genome wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing conservation efforts.
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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, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Michael J Moore, 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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Additional file 6: of Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family
2017Co-Authors: Yanxia Sun, Michael Moore, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Hengchang WangAbstract:Repeats âĽ30 bp in the plastomes of seven other Ranunculales species. (DOC 30 kb
Linsen Yang - One of the best experts on this subject based on the ideXlab platform.
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genomic insights into adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
New Phytologist, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong ZhangAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical for understanding the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as the genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome-environment association analyses identified 16 putatively adaptive loci related mainly to biotic and abiotic stress resistance. Our genome-wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing future conservation efforts.
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genome wide sequencing provides evidence of adaptation to heterogeneous environments for the ancient relictual circaeaster agrestis circaeasteraceae Ranunculales
bioRxiv, 2020Co-Authors: Xu Zhang, Yanxia Sun, Nan Lin, Linsen Yang, Jacob B Landis, Jianwen Zhang, Huajie Zhang, Rui Guo, Yonghong Zhang, Tao DengAbstract:Investigating the interaction between environmental heterogeneity and local adaptation is critical to understand the evolutionary history of a species, providing the premise for studying the response of organisms to rapid climate change. However, for most species how exactly the spatial heterogeneity promotes population divergence and how genomic variations contribute to adaptive evolution remain poorly understood. We examine the contributions of geographical and environmental variables to population divergence of the relictual, alpine herb Circaeaster agrestis, as well as genetic basis of local adaptation using RAD-seq and plastome data. We detected significant genetic structure with an extraordinary disequilibrium of genetic diversity among regions, and signals of isolation-by-distance along with isolation-by-resistance. The populations were estimated to begin diverging in the late Miocene, along with a possible ancestral distribution of the Hengduan Mountains and adjacent regions. Both environmental gradient and redundancy analyses revealed significant association between genetic variation and temperature variables. Genome‐environment association analyses identified 16 putatively adaptive loci related to biotic and abiotic stress resistance. Our genome wide data provide new insights into the important role of environmental heterogeneity in shaping genetic structure, and access the footprints of local adaptation in an ancient relictual species, informing conservation efforts.
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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, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Michael J Moore, 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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Additional file 6: of Complete plastome sequencing of both living species of Circaeasteraceae (Ranunculales) reveals unusual rearrangements and the loss of the ndh gene family
2017Co-Authors: Yanxia Sun, Michael Moore, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Hengchang WangAbstract:Repeats âĽ30 bp in the plastomes of seven other Ranunculales species. (DOC 30 kb
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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, Nan Lin, Kole Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Michael J Moore, 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
