Pryer Lab Pryer Lab
Arts & Sciences
Duke University

 HOME > Arts & Sciences > Pryer Lab    Search Help Login pdf version printable version 
Webpage

Pryer Lab : Publications since January 2017

List all publications in the database.    :chronological  alphabetical  combined listing:
%% Pryer, Kathleen M.   
@article{fds330472,
   Author = {Dijkhuizen, LW and Brouwer, P and Bolhuis, H and Reichart, G-J and Koppers, N and Huettel, B and Bolger, AM and Li, F-W and Cheng, S and Liu,
             X and Wong, GK-S and Pryer, K and Weber, A and Bräutigam, A and Schluepmann, H},
   Title = {Is there foul play in the leaf pocket? The metagenome of
             floating fern Azolla reveals endophytes that do not fix N2
             but may denitrify.},
   Journal = {New Phytologist},
   Volume = {217},
   Number = {1},
   Pages = {453-466},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1111/nph.14843},
   Abstract = {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.},
   Doi = {10.1111/nph.14843},
   Key = {fds330472}
}

@article{fds332387,
   Author = {Song, M and Kuo, L-Y and Huiet, L and Pryer, KM and Rothfels, CJ and Li,
             F-W},
   Title = {A novel chloroplast gene reported for flagellate
             plants.},
   Journal = {American journal of botany},
   Volume = {105},
   Number = {1},
   Pages = {117-121},
   Year = {2018},
   Month = {January},
   url = {http://dx.doi.org/10.1002/ajb2.1010},
   Abstract = {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.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.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.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.},
   Doi = {10.1002/ajb2.1010},
   Key = {fds332387}
}

@article{fds322311,
   Author = {Rothfels, CJ and Pryer, KM and Li, F-W},
   Title = {Next-generation polyploid phylogenetics: rapid resolution of
             hybrid polyploid complexes using PacBio single-molecule
             sequencing.},
   Journal = {New Phytologist},
   Volume = {213},
   Number = {1},
   Pages = {413-429},
   Year = {2017},
   Month = {January},
   url = {http://dx.doi.org/10.1111/nph.14111},
   Abstract = {Difficulties in generating nuclear data for polyploids have
             impeded phylogenetic study of these groups. We describe a
             high-throughput protocol and an associated bioinformatics
             pipeline (Pipeline for Untangling Reticulate Complexes
             (Purc)) that is able to generate these data quickly and
             conveniently, and demonstrate its efficacy on accessions
             from the fern family Cystopteridaceae. We conclude with a
             demonstration of the downstream utility of these data by
             inferring a multi-labeled species tree for a subset of our
             accessions. We amplified four c. 1-kb-long nuclear loci and
             sequenced them in a parallel-tagged amplicon sequencing
             approach using the PacBio platform. Purc infers the final
             sequences from the raw reads via an iterative approach that
             corrects PCR and sequencing errors and removes PCR-mediated
             recombinant sequences (chimeras). We generated data for all
             gene copies (homeologs, paralogs, and segregating alleles)
             present in each of three sets of 50 mostly polyploid
             accessions, for four loci, in three PacBio runs (one run per
             set). From the raw sequencing reads, Purc was able to
             accurately infer the underlying sequences. This approach
             makes it easy and economical to study the phylogenetics of
             polyploids, and, in conjunction with recent analytical
             advances, facilitates investigation of broad patterns of
             polyploid evolution.},
   Doi = {10.1111/nph.14111},
   Key = {fds322311}
}


Duke University * Arts & Sciences * Pryer Lab * Director * Members * Reload * Login