Browsing by Author "Lopez-Bautista, Juan M."

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    The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin
    (BMC, 2015) Leliaert, Frederik; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Ghent University
    Background: Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified). Results: Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta. Conclusions: The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae.
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    Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.
    (Nature Portfolio, 2016) Leliaert, Frederik; Tronholm, Ana; Lemieux, Claude; Turmel, Monique; DePriest, Michael S.; Bhattacharya, Debashish; Karol, Kenneth G.; Fredericq, Suzanne; Zechman, Frederick W.; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Ghent University; Florida International University; Laval University; Rutgers State University New Brunswick; New York Botanical Garden; University of Louisiana Lafayette; California State Polytechnic University, Humboldt
    The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.
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    The Complete Chloroplast and Mitochondrial Genomes of the Green Macroalga Ulva sp UNA00071828 (Ulvophyceae, Chlorophyta)
    (PLOS, 2015) Melton, James T., III; Leliaert, Frederik; Tronholm, Ana; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Ghent University; Smithsonian Institution; Smithsonian National Museum of Natural History
    Sequencing mitochondrial and chloroplast genomes has become an integral part in understanding the genomic machinery and the phylogenetic histories of green algae. Previously, only three chloroplast genomes (Oltmannsiellopsis viridis, Pseudendoclonium akinetum, and Bryopsis hypnoides) and two mitochondrial genomes (O. viridis and P. akinetum) from the class Ulvophyceae have been published. Here, we present the first chloroplast and mitochondrial genomes from the ecologically and economically important marine, green algal genus Ulva. The chloroplast genome of Ulva sp. was 99,983 bp in a circular-mapping molecule that lacked inverted repeats, and thus far, was the smallest ulvophycean plastid genome. This cpDNA was a highly compact, AT-rich genome that contained a total of 102 identified genes (71 protein-coding genes, 28 tRNA genes, and three ribosomal RNA genes). Additionally, five introns were annotated in four genes: atpA (1), petB (1), psbB (2), and rrl (1). The circular-mapping mitochondrial genome of Ulva sp. was 73,493 bp and follows the expanded pattern also seen in other ulvophyceans and trebouxiophyceans. The Ulva sp. mtDNA contained 29 protein-coding genes, 25 tRNA genes, and two rRNA genes for a total of 56 identifiable genes. Ten introns were annotated in this mtDNA: cox1 (4), atp1 (1), nad3 (1), nad5 (1), and rrs (3). Double-cut-and-join (DCJ) values showed that organellar genomes across Chlorophyta are highly rearranged, in contrast to the highly conserved organellar genomes of the red algae (Rhodophyta). A phylogenomic investigation of 51 plastid protein-coding genes showed that Ulvophyceae is not monophyletic, and also placed Oltmannsiellopsis (Oltmannsiellopsidales) and Tetraselmis (Chlorodendrophyceae) closely to Ulva (Ulvales) and Pseudendoclonium (Ulothrichales).
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    Counter-balancing mechanism for improving independence when using an exoskeleton
    (University of Alabama Libraries, 2013) Lathan, Drew; Todd, Beth A.; University of Alabama Tuscaloosa
    An exoskeleton is a robotic device used in assisting paraplegics with standing and walking. Existing designs use a series of DC motors and brakes to move the different parts of the device. Some exoskeletons mimic the musculoskeletal system by sending signals to a computer that tells the motors to rotate the knee, ankle, and hip joints appropriately for correct forward movement of the device. Users of the devices have a walker or crutches with controls to aid in balance. The goal of this project is to provide complete independence by removing the need for these walking aids. A new leg orthotic has been designed that may be implemented on any exoskeleton device to maintain balance in the fore-aft direction. A series of fast-acting electric actuators respond to the individual's movements. If at any point the device begins to tip, the actuators engage in such a way that the user's leg is brought back to an up-right position allowing balance to be recovered. As this movement takes place, the normal actions of the device's DC motors and brakes are also engaged to avoid falling (the reactions from the motors and brakes are already a feature of current exoskeleton designs.) This is a counter-balancing mechanism and could provide more independence to paraplegics in the future.
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    The Organellar Genomes of Melanthalia Abscissa and Polyopes Polyideoides (Rhodophyta, Florideophyceae)
    (University of Alabama Libraries, 2024) Freiler, Matthew Nance; Lopez-Bautista, Juan M.
    Florideophyceae is the most species rich red algal class, including large numbers of well-studied, economically important species and lesser-known clades. We present the complete plastid and mitochondrial genome assemblies of two Florideophycean species, Melanthalia abscissa (Gracilariaceae) and Polyopes polyideoides (Halymeniaceae). We identified more large-scale rearrangements within the plastid genomes of Gracilariales than within Halymeniales. Maximum likelihood phylogenies using rbcL data support the placement of both M. abscissa and P. polyideoides samples in monophyletic genera. However, not all genera within Halymeniales were recovered as monophyletic. Sequences that appear to be derived from red algal plasmids were identified within the plastid genome of M. abscissa. Determining the presence or absence of plasmid-derived sequences in the P. polyideoides plastome is more difficult due to a lack of publicly available data for Halymeniaceae. The addition of the sequences produced by this study will support further phylogenetic and systematic research on these Rhodophytan genera and orders. Keywords: plastid genome, mitochondria, phylogeny, rbcL
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    The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)
    (PLOS, 2013) DePriest, Michael S.; Bhattacharya, Debashish; Lopez-Bautista, Juan M.; University of Alabama Tuscaloosa; Rutgers State University New Brunswick
    The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M. Lin & H.-Y. Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.