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Find video protocols related to scientific articles indexed in Pubmed.
Between two fern genomes.
Gigascience
PUBLISHED: 01-01-2014
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Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Jo Ann Banks, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L Bowman, Michael Gribskov, Claude dePamphilis, Victor A Albert, Naoki Aono, Tsuyoshi Aoyama, Barbara A Ambrose, Neil W Ashton, Michael J Axtell, Elizabeth Barker, Michael S Barker, Jeffrey L Bennetzen, Nicholas D Bonawitz, Clint Chapple, Chaoyang Cheng, Luiz Gustavo Guedes Corrêa, Michael Dacre, Jeremy DeBarry, Ingo Dreyer, Marek Eliáš, Eric M Engstrom, Mark Estelle, Liang Feng, Cédric Finet, Sandra K Floyd, Wolf B Frommer, Tomomichi Fujita, Lydia Gramzow, Michael Gutensohn, Jesper Harholt, Mitsuru Hattori, Alexander Heyl, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Kenneth G Karol, Barbara Koehler, Uener Kolukisaoglu, Minoru Kubo, Tetsuya Kurata, Sylvie Lalonde, Kejie Li, Ying Li, Amy Litt, Eric Lyons, Gerard Manning, Takeshi Maruyama, Todd P Michael, Koji Mikami, Saori Miyazaki, Shin-Ichi Morinaga, Takashi Murata, Bernd Mueller-Roeber, David R Nelson, Mari Obara, Yasuko Oguri, Richard G Olmstead, Naoko Onodera, Bent Larsen Petersen, Birgit Pils, Michael Prigge, Stefan A Rensing, Diego Mauricio Riaño-Pachón, Alison W Roberts, Yoshikatsu Sato, Henrik Vibe Scheller, Burkhard Schulz, Christian Schulz, Eugene V Shakirov, Nakako Shibagaki, Naoki Shinohara, Dorothy E Shippen, Iben Sørensen, Ryo Sotooka, Nagisa Sugimoto, Mamoru Sugita, Naomi Sumikawa, Milos Tanurdzic, Günter Theißen, Peter Ulvskov, Sachiko Wakazuki, Jing-Ke Weng, William W G T Willats, Daniel Wipf, Paul G Wolf, Lixing Yang, Andreas D Zimmer, Qihui Zhu, Therese Mitros, Uffe Hellsten, Dominique Loqué, Robert Otillar, Asaf Salamov, Jeremy Schmutz, Harris Shapiro, Erika Lindquist, Susan Lucas, Daniel Rokhsar, Igor V Grigoriev.
Science
PUBLISHED: 05-05-2011
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Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
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A vacuolar arsenite transporter necessary for arsenic tolerance in the arsenic hyperaccumulating fern Pteris vittata is missing in flowering plants.
Plant Cell
PUBLISHED: 06-08-2010
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The fern Pteris vittata tolerates and hyperaccumulates exceptionally high levels of the toxic metalloid arsenic, and this trait appears unique to the Pteridaceae. Once taken up by the root, arsenate is reduced to arsenite as it is transported to the lamina of the frond, where it is stored in cells as free arsenite. Here, we describe the isolation and characterization of two P. vittata genes, ACR3 and ACR3;1, which encode proteins similar to the ACR3 arsenite effluxer of yeast. Pv ACR3 is able to rescue the arsenic-sensitive phenotypes of yeast deficient for ACR3. ACR3 transcripts are upregulated by arsenic in sporophyte roots and gametophytes, tissues that directly contact soil, whereas ACR3;1 expression is unaffected by arsenic. Knocking down the expression of ACR3, but not ACR3;1, in the gametophyte results in an arsenite-sensitive phenotype, indicating that ACR3 plays a necessary role in arsenic tolerance in the gametophyte. We show that ACR3 localizes to the vacuolar membrane in gametophytes, indicating that it likely effluxes arsenite into the vacuole for sequestration. Whereas single-copy ACR3 genes are present in moss, lycophytes, other ferns, and gymnosperms, none are present in angiosperms. The duplication of ACR3 in P. vittata and the loss of ACR3 in angiosperms may explain arsenic tolerance in this unusual group of ferns while precluding the same trait in angiosperms.
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Selaginella and 400 million years of separation.
Annu Rev Plant Biol
PUBLISHED: 07-07-2009
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Selaginella (spikemoss) is an enigma in the plant kingdom. Although a fascination to botanists at the turn of the twentieth century, members of this genus are unremarkable in appearance, never flower, and are of no agronomic value. However, members of this genus are relicts from ancient times, and one has to marvel at how this genus has survived virtually unchanged in appearance for hundreds of millions of years. In light of the recent completion of the Selaginella moellendorffii genome sequence, this review is intended to survey what is known about Selaginella, with a special emphasis on recent inquiries into its unique biology and importance in understanding the early evolution of vascular plants.
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The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall.
PLoS ONE
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Spike mosses are among the most basal vascular plants, and one species, Selaginella moellendorffii, was recently selected for full genome sequencing by the Joint Genome Institute (JGI). Glycosyltransferases (GTs) are involved in many aspects of a plant life, including cell wall biosynthesis, protein glycosylation, primary and secondary metabolism. Here, we present a comparative study of the S. moellendorffii genome across 92 GT families and an additional family (DUF266) likely to include GTs. The study encompasses the moss Physcomitrella patens, a non-vascular land plant, while rice and Arabidopsis represent commelinid and non-commelinid seed plants. Analysis of the subset of GT-families particularly relevant to cell wall polysaccharide biosynthesis was complemented by a detailed analysis of S. moellendorffii cell walls. The S. moellendorffii cell wall contains many of the same components as seed plant cell walls, but appears to differ somewhat in its detailed architecture. The S. moellendorffii genome encodes fewer GTs (287 GTs including DUF266s) than the reference genomes. In a few families, notably GT51 and GT78, S. moellendorffii GTs have no higher plant orthologs, but in most families S. moellendorffii GTs have clear orthologies with Arabidopsis and rice. A gene naming convention of GTs is proposed which takes orthologies and GT-family membership into account. The evolutionary significance of apparently modern and ancient traits in S. moellendorffii is discussed, as is its use as a reference organism for functional annotation of GTs.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.