8 results on '"Session, Adam M"'
Search Results
2. Genome biology of the paleotetraploid perennial biomass crop Miscanthus
- Author
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Mitros, Therese, Session, Adam M, James, Brandon T, Wu, Guohong Albert, Belaffif, Mohammad B, Clark, Lindsay V, Shu, Shengqiang, Dong, Hongxu, Barling, Adam, Holmes, Jessica R, Mattick, Jessica E, Bredeson, Jessen V, Liu, Siyao, Farrar, Kerrie, Głowacka, Katarzyna, Jeżowski, Stanisław, Barry, Kerrie, Chae, Won Byoung, Juvik, John A, Gifford, Justin, Oladeinde, Adebosola, Yamada, Toshihiko, Grimwood, Jane, Putnam, Nicholas H, De Vega, Jose, Barth, Susanne, Klaas, Manfred, Hodkinson, Trevor, Li, Laigeng, Jin, Xiaoli, Peng, Junhua, Yu, Chang Yeon, Heo, Kweon, Yoo, Ji Hye, Ghimire, Bimal Kumar, Donnison, Iain S, Schmutz, Jeremy, Hudson, Matthew E, Sacks, Erik J, Moose, Stephen P, Swaminathan, Kankshita, and Rokhsar, Daniel S
- Subjects
Biotechnology ,Human Genome ,Genetics ,Affordable and Clean Energy ,Biomass ,Chromosomes ,Plant ,DNA Transposable Elements ,Diploidy ,Evolution ,Molecular ,Gene Expression Regulation ,Plant ,Genetic Variation ,Genome ,Plant ,Genomics ,Models ,Genetic ,Phylogeny ,Poaceae ,Polyploidy ,Saccharum ,Seasons ,Sorghum - Abstract
Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.
- Published
- 2020
3. Kif2a Scales Meiotic Spindle Size in Hymenochirus boettgeri
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Miller, Kelly E, Session, Adam M, and Heald, Rebecca
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Underpinning research ,1.1 Normal biological development and functioning ,Generic health relevance ,Amphibian Proteins ,Animals ,Anura ,Cell Cycle Proteins ,Female ,Katanin ,Kinesins ,Microtubule-Associated Proteins ,Spindle Apparatus ,Hymenochirus boettgeri ,TPX2 ,Xenopus laevis ,Xenopus tropicalis ,egg extract ,katanin ,kif2a ,meiotic spindle ,sub cellular scaling ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Psychology - Abstract
Size is a fundamental feature of biological systems that affects physiology at all levels. For example, the dynamic, microtubule-based spindle that mediates chromosome segregation scales to a wide range of cell sizes across different organisms and cell types. Xenopus frog species possess a variety of egg and meiotic spindle sizes, and differences in activities or levels of microtubule-associated proteins in the egg cytoplasm between Xenopus laevis and Xenopus tropicalis have been shown to account for spindle scaling [1]. Increased activity of the microtubule severing protein katanin scales the X. tropicalis spindle smaller compared to X. laevis [2], as do elevated levels of TPX2, a protein that enriches the cross-linking kinesin-5 motor Eg5 at spindle poles [3]. To examine the conservation of spindle scaling mechanisms more broadly across frog species, we have utilized the tiny, distantly related Pipid frog Hymenochirus boettgeri. We find that egg extracts from H. boettgeri form meiotic spindles similar in size to X. tropicalis but that TPX2 and katanin-mediated scaling is not conserved. Instead, the microtubule depolymerizing motor protein kif2a functions to modulate spindle size. H. boettgeri kif2a possesses an activating phosphorylation site that is absent from X. laevis. Comparison of katanin and kif2a phosphorylation sites across a variety of species revealed strong evolutionary conservation, with X. laevis and X. tropicalis possessing distinct and unique alterations. Our study highlights the diversity and complexity of spindle assembly and scaling mechanisms, indicating that there is more than one way to assemble a spindle of a particular size.
- Published
- 2019
4. A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis
- Author
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Mitros, Therese, Lyons, Jessica B, Session, Adam M, Jenkins, Jerry, Shu, Shengquiang, Kwon, Taejoon, Lane, Maura, Ng, Connie, Grammer, Timothy C, Khokha, Mustafa K, Grimwood, Jane, Schmutz, Jeremy, Harland, Richard M, and Rokhsar, Daniel S
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Generic health relevance ,Animals ,Chromosome Mapping ,Chromosomes ,Gene Expression Profiling ,Genome ,Humans ,Molecular Sequence Annotation ,Xenopus ,Genome assembly ,Genetic mapping ,Comparative genomics ,Pigmentation ,Sex determination ,Gene expression analysis ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.
- Published
- 2019
5. Genome evolution in the allotetraploid frog Xenopus laevis
- Author
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Session, Adam M, Uno, Yoshinobu, Kwon, Taejoon, Chapman, Jarrod A, Toyoda, Atsushi, Takahashi, Shuji, Fukui, Akimasa, Hikosaka, Akira, Suzuki, Atsushi, Kondo, Mariko, van Heeringen, Simon J, Quigley, Ian, Heinz, Sven, Ogino, Hajime, Ochi, Haruki, Hellsten, Uffe, Lyons, Jessica B, Simakov, Oleg, Putnam, Nicholas, Stites, Jonathan, Kuroki, Yoko, Tanaka, Toshiaki, Michiue, Tatsuo, Watanabe, Minoru, Bogdanovic, Ozren, Lister, Ryan, Georgiou, Georgios, Paranjpe, Sarita S, van Kruijsbergen, Ila, Shu, Shengquiang, Carlson, Joseph, Kinoshita, Tsutomu, Ohta, Yuko, Mawaribuchi, Shuuji, Jenkins, Jerry, Grimwood, Jane, Schmutz, Jeremy, Mitros, Therese, Mozaffari, Sahar V, Suzuki, Yutaka, Haramoto, Yoshikazu, Yamamoto, Takamasa S, Takagi, Chiyo, Heald, Rebecca, Miller, Kelly, Haudenschild, Christian, Kitzman, Jacob, Nakayama, Takuya, Izutsu, Yumi, Robert, Jacques, Fortriede, Joshua, Burns, Kevin, Lotay, Vaneet, Karimi, Kamran, Yasuoka, Yuuri, Dichmann, Darwin S, Flajnik, Martin F, Houston, Douglas W, Shendure, Jay, DuPasquier, Louis, Vize, Peter D, Zorn, Aaron M, Ito, Michihiko, Marcotte, Edward M, Wallingford, John B, Ito, Yuzuru, Asashima, Makoto, Ueno, Naoto, Matsuda, Yoichi, Veenstra, Gert Jan C, Fujiyama, Asao, Harland, Richard M, Taira, Masanori, and Rokhsar, Daniel S
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,Animals ,Chromosomes ,Conserved Sequence ,DNA Transposable Elements ,Diploidy ,Evolution ,Molecular ,Female ,Gene Deletion ,Gene Expression Profiling ,Genome ,Karyotype ,Molecular Sequence Annotation ,Mutagenesis ,Phylogeny ,Pseudogenes ,Tetraploidy ,Xenopus ,Xenopus laevis ,General Science & Technology - Abstract
To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
- Published
- 2016
6. Transposon signatures of allopolyploid genome evolution
- Author
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Session, Adam M., primary and Rokhsar, Daniel S., additional
- Published
- 2023
- Full Text
- View/download PDF
7. Genomic Analysis of the Allotetraploid Frog, Xenopus laevis
- Author
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Session, Adam M
- Subjects
Bioinformatics ,Genetics ,Evolution & development ,Duplication ,Homeologs ,Polyploidy ,Xenopus - Abstract
Duplication has long been recognized as an evolutionary source of novelty. The relaxation of purifying selection following duplication allows for normally deleterious mutations to persist long enough to give rise to novel phenotypes. Whole-genome duplications (WGDs) are a specific type of duplication, in which a species suddenly finds itself with two copies of all of its genomic loci. While the fate of most of the duplicated loci is to be lost, those that persist are thought to underlie the innovations seen in groups with a history of polyploidy, such as flowering plants, yeast, Paramecium, and vertebrates. These ancient events give us an idea of how WGDs can drive the radiation of large and diverse phyla, but do not give us any information on the genomic response immediately following polyploidy. This thesis provides insights into the origins of polyploidy and its effects on genome dynamics.There are two models for the mechanism of polyploidy: autopolyploidy and allopolyploidy. Autopolyploids are formed by doubling the somatic chromosomes in the zygote or early embryo. Allopolyploids are formed by the hybridization of two related, but genetically distinct, species, followed by chromosome doubling. If there are no extant diploid relatives, it can be difficult to distinguish between these two models. One feature of allopolyploids is the lack of recombination between their homeologous chromosomes. The end result is that any markers that were unique to each species while apart, such as transposable element subfamilies, will be asymmetrically distributed on the progenitor chromosomes in an organism that recently underwent a WGD.Xenopus laevis is an important vertebrate model in developmental and cell biology that has experienced a recent WGD (~40 million years ago [MYA], based on cDNA alignments (Hellsten, 2007). Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. Comparative analysis of these two frog genomes gives us an excellent opportunity to study genome dynamics following whole genome duplication. The discovery of asymmetrically distributed transposon subfamilies supports the model that cross-species hybridization through allotetraploidy is the mechanism underlying the polyploid Xenopus radiation. Thus, the sub-genome sequence divergence of 40 MYA dates the divergence of the progenitor species, not the hybridization event. The asymmetric distribution of these elements between homeologous sequences allows us to assign chromosomes to progenitor species, named “A” and “B”, making X. laevis a unique system to study sub-genome-specific evolution. The wealth of transcriptome and epigenetic data available for Xenopus allows me to assay how these genomic changes affect gene expression as well as gene retention. The combination of these resources with genomic data gives me the resolution needed to date the hybridization both by studying the decay of unitary pseudogenes and by comparative analysis of the transposable elements discussed above.The sub-genome from progenitor species “A” has more assembled length, longer chromosomes, a higher rate of gene retention, and higher average expression in the adult frog. The B sub-genome has higher synonymous and nonsynonymous mutation rates. The chromosomes orthologous to X. tropicalis 9 and 10 are fused in both sub-genomes of X. laevis, forming homeologous chromosomes 15 and 18, and deviate from the A/B trends discussed above. The regions of these X. laevis chromosomes orthologous to X. tropicalis chromosome 10 have a lower density of diagnostic repeats, no sub-genome bias in gene retention, and have a higher silent substitution rate. This divergence from the rest of the genome is not shared by the regions orthologous to X. tropicalis 9. I hypothesize that the short length of X. tropicalis 10 plays a role in these deviations due to a higher rate of gene conversion on shorter chromosomes.
- Published
- 2015
8. Genome evolution in the allotetraploid frog Xenopus laevis
- Author
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Session, Adam M., Uno, Yoshinobu, Kwon, Taejoon, Suzuki, Atsushi, Georgiou, G., Paranjpe, S.S., Kruijsbergen, I. van, Ueno, Naoto, Matsuda, Yoichi, Veenstra, G.J.C., Taira, Masanori, Rokhsar, Daniel S., Session, Adam M., Uno, Yoshinobu, Kwon, Taejoon, Suzuki, Atsushi, Georgiou, G., Paranjpe, S.S., Kruijsbergen, I. van, Ueno, Naoto, Matsuda, Yoichi, Veenstra, G.J.C., Taira, Masanori, and Rokhsar, Daniel S.
- Abstract
19 oktober 2016, Contains fulltext : 181014.pdf (publisher's version ) (Open Access)
- Published
- 2016
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