Browsing by Author "Li, F"

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Open Access
A first glimpse at genes important to the Azolla–Nostoc symbiosis
(Symbiosis, 2019-01-01) Eily, AN; Pryer, KM; Li, F
© 2019, Springer Nature B.V. Azolla is a small genus of diminutive aquatic ferns with a surprisingly vast potential to benefit the environment and agriculture, as well as to provide insight into the evolution of plant-cyanobacterial symbioses. This capability is derived from the unique relationship Azolla spp. have with their obligate, nitrogen-fixing cyanobacterial symbiont, Nostoc azollae, that resides in their leaves. Although previous work has specified the importance of the exchange of ammonium and sucrose metabolites between these two partners, we have yet to determine the underlying molecular mechanisms that make this symbiosis so successful. The newly sequenced and annotated reference genome of Azolla filiculoides has allowed us to investigate gene expression profiles of A. filiculoides—both with and without its obligate cyanobiont, N. azollae—revealing genes potentially essential to the Azolla-Nostoc symbiosis. We observed the absence of differentially expressed glutamine synthetase (GS) and glutamate synthase (GOGAT) genes, leading to questions about how A. filiculoides regulates the machinery it uses for nitrogen assimilation. Ushering A. filiculoides into the era of transcriptomics sets the stage to truly begin to understand the uniqueness of the Azolla-Nostoc symbiosis.
Open Access
A novel chloroplast gene reported for flagellate plants.
(American journal of botany, 2018-01) Song, M; Kuo, L; Huiet, L; Pryer, KM; Rothfels, CJ; Li, F
PREMISE OF THE STUDY:Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS:We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. KEY RESULTS:The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein-encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts-a hallmark of protein-coding genes in fern plastomes. CONCLUSIONS:The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA-editing sites, suggests that ycf94 is a protein-coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.
Open Access
A step-by-step protocol for meiotic chromosome counts in flowering plants: A powerful and economical technique revisited.
(Applications in plant sciences, 2020-04-23) Windham, MD; Pryer, KM; Poindexter, DB; Li, F; Rothfels, CJ; Beck, JB
Premise:Counting chromosomes is a fundamental botanical technique, yet it is often intimidating and increasingly sidestepped. Once mastered, the basic protocol can be applied to a broad range of taxa and research questions. It also reveals an aspect of the plant genome that is accessible with only the most basic of resources-access to a microscope with 1000× magnification is the most limiting factor. Methods and Results:Here we provide a detailed protocol for choosing, staining, and squashing angiosperm pollen mother cells. The protocol is supplemented by figures and two demonstration videos. Conclusions:The protocol we provide will hopefully demystify and reinvigorate a powerful and once commonplace botanical technique that is available to researchers regardless of their location and resources.
Open Access
A worldwide phylogeny of Adiantum (Pteridaceae) reveals remarkable convergent evolution in leaf blade architecture
(Taxon, 2018-06-01) Huiet, L; Li, F; Kao, T; Prado, J; Smith, AR; Schuettpelz, E; Pryeri, KM
© International Association for Plant Taxonomy (IAPT) 2018, All rights reserved. Adiantum is among the most distinctive and easily recognized leptosporangiate fern genera. Despite encompassing an astonishing range of leaf complexity, all species of Adiantum share a unique character state not observed in other ferns: sporangia borne directly on the reflexed leaf margin or “false indusium” (pseudoindusium). The over 200 species of Adiantum span six continents and are nearly all terrestrial. Here, we present one of the most comprehensive phylogenies for any large (200+ spp.) monophyletic, subcosmopolitan genus of ferns to date. We build upon previous datasets, providing new data from four plastid markers (rbcL, atpA, rpoA, chlN) for 146 taxa. All sampled taxa can be unequivocally assigned to one of nine robustly supported clades. Although some of these unite to form larger, well-supported lineages, the backbone of our phylogeny has several short branches and generally weak support, making it difficult to accurately assess deep relationships. Our maximum likelihood-based ancestral character state reconstructions of leaf blade architecture reveal remarkable convergent evolution across multiple clades for nearly all leaf forms. A single unique synapomorphy—leaves once-pinnate, usually with prolonged rooting tips—defines the philippense clade. Although a rare occurrence in Adiantum, simple leaves occur in three distinct clades (davidii, philippense, peruvianum). Most taxa have leaves that are more than once-pinnate, and only a few of these (in the formosum and pedatum clades) exhibit the distinct pseudopedate form. Distributional ranges for each of the terminal taxa show that most species (75%) are restricted to only one of six major biogeographical regions. Forty-eight of our sampled species (nearly one-third) are endemic to South America.
Open Access
An Empirical Comparison of Multiple Imputation Methods for Categorical Data
(The American Statistician, 2017-04-03) Akande, O; Li, F; Reiter, J
© 2017 American Statistical Association. Multiple imputation is a common approach for dealing with missing values in statistical databases. The imputer fills in missing values with draws from predictive models estimated from the observed data, resulting in multiple, completed versions of the database. Researchers have developed a variety of default routines to implement multiple imputation; however, there has been limited research comparing the performance of these methods, particularly for categorical data. We use simulation studies to compare repeated sampling properties of three default multiple imputation methods for categorical data, including chained equations using generalized linear models, chained equations using classification and regression trees, and a fully Bayesian joint distribution based on Dirichlet process mixture models. We base the simulations on categorical data from the American Community Survey. In the circumstances of this study, the results suggest that default chained equations approaches based on generalized linear models are dominated by the default regression tree and Bayesian mixture model approaches. They also suggest competing advantages for the regression tree and Bayesian mixture model approaches, making both reasonable default engines for multiple imputation of categorical data. Supplementary material for this article is available online.
Open Access
An exploration into fern genome space
(Genome Biology and Evolution, 2015) Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE
Open Access
An Exploration into Fern Genome Space.
(Genome Biol Evol, 2015-08-26) Wolf, PG; Sessa, EB; Marchant, DB; Li, F; Rothfels, CJ; Sigel, EM; Gitzendanner, MA; Visger, CJ; Banks, JA; Soltis, DE
Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
Open Access
Bayesian variable selection in structured high-dimensional covariate spaces with applications in genomics
(Journal of the American Statistical Association, 2010-09-01) Li, F; Zhang, NR
We consider the problem of variable selection in regression modeling in high-dimensional spaces where there is known structure among the covariates. This is an unconventional variable selection problem for two reasons: (1) The dimension of the covariate space is comparable, and often much larger, than the number of subjects in the study, and (2) the covariate space is highly structured, and in some cases it is desirable to incorporate this structural information in to the model building process. We approach this problem through the Bayesian variable selection framework, where we assume that the covariates lie on an undirected graph and formulate an Ising prior on the model space for incorporating structural information. Certain computational and statistical problems arise that are unique to such high-dimensional, structured settings, the most interesting being the phenomenon of phase transitions. We propose theoretical and computational schemes to mitigate these problems. We illustrate our methods on two different graph structures: the linear chain and the regular graph of degree k. Finally, we use our methods to study a specific application in genomics: the modeling of transcription factor binding sites in DNA sequences. © 2010 American Statistical Association.
Open Access
Between two fern genomes
(GigaScience, 2014) Sessa, EB; Banks, JA; Barker, MS; Der, JP; Duffy, AM; Graham, SW; Hasebe, M; Langdale, J; Li, F; Marchant, DB
Open Access
Crowdfunding the Azolla fern genome project: a grassroots approach
(GigaScience, 2014) Li, F; Pryer, KM
Open Access
Do debit cards increase household spending? Evidence from a semiparametric causal analysis of a survey
(Annals of Applied Statistics, 2014-01-01) Mercatanti, A; Li, F
© Institute of Mathematical Statistics, 2014.Motivated by recent findings in the field of consumer science, this paper evaluates the causal effect of debit cards on household consumption using population-based data from the Italy Survey on Household Income and Wealth (SHIW). Within the Rubin Causal Model, we focus on the estimand of population average treatment effect for the treated (PATT). We consider three existing estimators, based on regression, mixed matching and regression, propensity score weighting, and propose a new doubly-robust estimator. Semiparametric specification based on power series for the potential outcomes and the propensity score is adopted. Cross-validation is used to select the order of the power series. We conduct a simulation study to compare the performance of the estimators. The key assumptions, overlap and unconfoundedness, are systematically assessed and validated in the application. Our empirical results suggest statistically significant positive effects of debit cards on the monthly household spending in Italy.
Open Access
E-Commerce and Industrial Upgrading in the Chinese Apparel Value Chain
(Journal of Contemporary Asia, 2019-01-01) Li, F; Frederick, S; Gereffi, G
© 2018, © 2018 Journal of Contemporary Asia. The economic and social gains from electronic commerce (e-commerce) that promote innovation, industry upgrading and economic growth have been widely discussed. China’s successful experience with e-commerce has had a positive effect in transforming consumer-goods sectors of the economy and motivating economic reform. This article looks at how e-commerce reduces barriers to entry and enables firms to move up the value chain by using the global value chain framework to analyse the impact of e-commerce on the upgrading trajectories and governance structures of China’s apparel industry. For large Chinese brands, e-commerce has enabled end-market diversification. For small- and medium-sized enterprises, e-commerce has facilitated entry with functional upgrading as well as end-market upgrading. In the “two-sided markets” created by platform companies, the “engaged consumers” are the demand side of this market, and “e-commerce focused apparel firms” are the supply side of the new market. Consumers and platforms are more directly involved in value creation within this emerging internet-based structure.
Open Access
Fern genomes elucidate land plant evolution and cyanobacterial symbioses.
(Nature plants, 2018-07-02) Li, F; Brouwer, P; Carretero-Paulet, L; Cheng, S; De Vries, J; Delaux, P; Eily, A; Koppers, N; Kuo, L; Li, Z
Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N2-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.
Open Access
Gaga, a new fern genus segregated from cheilanthes (pteridaceae)
(Systematic Botany, 2012-10-01) Li, F; Pryer, KM; Windham, MD
Ongoing molecular phylogenetic studies of cheilanthoid ferns confirm that the genus Cheilanthes (Pteridaceae) is polyphyletic. A monophyletic group of species within the hemionitid clade informally called the "C. marginata group" is here shown to be distinct from its closest relatives (the genus Aspidotis) and phylogenetically distant from the type species of Cheilanthes. This group is here segregated from Cheilanthes as the newly described genus, Gaga . In this study, we use molecular data from four DNA regions (plastid: matK, rbcL, trnG-R; and nuclear: gapCp) together with spore data to circumscribe the morphological and geographical boundaries of the new genus and investigate reticulate evolution within the group. Gaga is distinguished from Aspidotis by its rounded to attenuate (vs. mucronate) segment apices, minutely bullate margins of mature leaves (vs. smooth at 40 ×), and less prominently lustrous and striate adaxial blade surfaces. The new genus is distinguished from Cheilanthes s. s. by its strongly differentiated, inframarginal pseudoindusia, the production of 64 small or 32 large spores (vs. 32 small or 16 large) per sporangium, and usually glabrous leaf blades. A total of nineteen species are recognized within Gaga; seventeen new combinations are made, and two new species, Gaga germanotta and Gaga monstraparva , are described. © Copyright 2012 by the American Society of Plant Taxonomists.
Open Access
Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content.
(Genome biology and evolution, 2016-08-25) Li, F; Kuo, L; Pryer, KM; Rothfels, CJ
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution. Here we examine four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC into the IR during fern evolution. We use a model-based method, within a phylogenetic context, to test for substitution rate shifts. All four loci show a significant, 2- to 3-fold deceleration in their substitution rate following translocation into the IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we show that after translocation, the GC content of the third codon position and of the noncoding regions is significantly increased, implying that gene conversion within the IR is GC-biased. Taken together, our results suggest that the IR region not only reduces substitution rates, but also impacts nucleotide composition. This finding highlights a potential vulnerability of correlating substitution rate heterogeneity with organismal life history traits without knowledge of the underlying genome structure.
Open Access
Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.
(Proceedings of the National Academy of Sciences of the United States of America, 2014-05) Li, F; Villarreal, JC; Kelly, S; Rothfels, CJ; Melkonian, M; Frangedakis, E; Ruhsam, M; Sigel, EM; Der, JP; Pittermann, J
Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
Open Access
Hydrological Response of East China to the Variation of East Asian Summer Monsoon
(Advances in Meteorology, 2016-01-01) Li, F; Chen, D; Tang, Q; Li, W; Zhang, X
Copyright © 2016 Fuxing Li et al.The sensitivity of hydrologic variables in East China, that is, runoff, precipitation, evapotranspiration, and soil moisture to the fluctuation of East Asian summer monsoon (EASM), is evaluated by the Mann-Kendall correlation analysis on a spatial resolution of 1/4° in the period of 1952-2012. The results indicate remarkable spatial disparities in the correlation between the hydrologic variables and EASM. The regions in East China susceptible to hydrological change due to EASM fluctuation are identified. When the standardized anomaly of intensity index of EASM (EASMI) is above 1.00, the runoff of Haihe basin has increased by 49% on average, especially in the suburb of Beijing and Hebei province where the runoff has increased up to 105%. In contrast, the runoff in the basins of Haihe and Yellow River has decreased by about 27% and 17%, respectively, when the standardized anomaly of EASMI is below -1.00, which has brought severe drought to the areas since mid-1970s. The study can be beneficial for national or watershed agencies developing adaptive water management strategies in the face of global climate change.
Open Access
Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify.
(The New phytologist, 2018-01) Dijkhuizen, LW; Brouwer, P; Bolhuis, H; Reichart, G; Koppers, N; Huettel, B; Bolger, AM; Li, F; Cheng, S; Liu, X
Dinitrogen fixation by Nostoc azollae residing in specialized leaf pockets supports prolific growth of the floating fern Azolla filiculoides. To evaluate contributions by further microorganisms, the A. filiculoides microbiome and nitrogen metabolism in bacteria persistently associated with Azolla ferns were characterized. A metagenomic approach was taken complemented by detection of N2 O released and nitrogen isotope determinations of fern biomass. Ribosomal RNA genes in sequenced DNA of natural ferns, their enriched leaf pockets and water filtrate from the surrounding ditch established that bacteria of A. filiculoides differed entirely from surrounding water and revealed species of the order Rhizobiales. Analyses of seven cultivated Azolla species confirmed persistent association with Rhizobiales. Two distinct nearly full-length Rhizobiales genomes were identified in leaf-pocket-enriched samples from ditch grown A. filiculoides. Their annotation revealed genes for denitrification but not N2 -fixation. 15 N2 incorporation was active in ferns with N. azollae but not in ferns without. N2 O was not detectably released from surface-sterilized ferns with the Rhizobiales. N2 -fixing N. azollae, we conclude, dominated the microbiome of Azolla ferns. The persistent but less abundant heterotrophic Rhizobiales bacteria possibly contributed to lowering O2 levels in leaf pockets but did not release detectable amounts of the strong greenhouse gas N2 O.
Open Access
Maidenhair ferns, adiantum, are indeed monophyletic and sister to shoestring ferns, vittarioids (Pteridaceae)
(Systematic Botany, 2016-01-01) Pryer, KM; Huiet, L; Li, F; Rothfels, CJ; Schuettpelz, E
© 2016 by the American Society of Plant Taxonomists. Across the tree of life, molecular phylogenetic studies often reveal surprising relationships between taxa with radically different morphologies that have long obscured their close affiliations. A spectacular botanical example is Rafflesia, a holoparasite that produces the largest flowers in the world, but that evolved from tiny-flowered ancestors within the Euphorbiaceae. Outside of parasitic lineages, such abrupt transformations are rarely seen. One exception involves the "maidenhair ferns" (Adiantum), which are quintessential ferns: beautifully dissected, terrestrial, and shade loving. The closely related "shoestring ferns" (vittarioids), in contrast, have an extremely simplified morphology, are canopy-dwelling epiphytes, and exhibit greatly accelerated rates of molecular evolution. While Adiantum and the vittarioids together have been shown to form a robust monophyletic group (adiantoids), there remain unanswered questions regarding the monophyly of Adiantum and the evolutionary history of the vittarioids. Here we review recent phylogenetic evidence suggesting support for the monophyly of Adiantum, and analyze new plastid data to confirm this result. We find that Adiantum is monophyletic and sister to the vittarioids. With this robust phylogenetic framework established for the broadest relationships in the adiantoid clade, we can now focus on understanding the evolutionary processes associated with the extreme morphological, ecological, and genetic transitions that took place within this lineage.
Open Access
NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches
(Nature communications, 2019) Yang, EJ; Yoo, CY; Liu, J; Wang, H; Cao, J; Li, F; Pryer, KM; Sun, T; Weigel, D; Zhou, P

Browsing by Author "Li, F"

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