The Poplar Genome PDF Download

Author: Ilga Porth
Publisher: Springer Nature
ISBN: 3031507878
Category :
Languages : en
Pages : 247

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Author: C. P. Joshi
Publisher: CRC Press
ISBN: 1439869170
Category : Science
Languages : en
Pages : 396

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Book Description
Written by researchers representing six countries and 28 institutions, this book highlights the development of the genus Populus as a model organism for tree genomics. Reflecting an impressive depth of coverage, the contributors' thorough reviews and analyses of Populus genomics provide insight into future discoveries about the basic biology of thi

Author: Stefan Jansson
Publisher: Springer
ISBN: 1441915419
Category : Science
Languages : en
Pages : 384

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Book Description
Genetics and Genomics of Populus provides an indepth description of the genetic and genomic tools and approaches for Populus, examines the biology that has been elucidated using genomics, and looks to the future of this unique model plant. This volume is designed to serve both experienced Populus researchers and newcomers to the field. Contributors to the volume are a blend of researchers, some who have spent most of their research career on Populus and others that have moved to Populus from other model systems. Research on Populus forms a useful complement to research on Arabidopsis. In fact, many plant species found in nature are – in terms of the life history and genetics – more similar to Populus than to Arabidopsis. Thus, the genetic and genomic strategies and tools developed by the Populus community, and showcased in this volume, will hopefully provide inspiration for researchers working in other, less well developed, systems.

Author: National Research Council Canada
Publisher: NRC Research Press
ISBN: 9780660165066
Category : Nature
Languages : en
Pages : 560

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Book Description
"Poplar is increasingly recognized as an excellent model tree for the study of tree growth and its underlying physiology and genetics. By studying trees of the genus Populus (poplars, cottonwoods, aspens), which in their native ecosystems play a major role in the re-colonization of sites after disturbances, new insights have been gained into plantation culture and the development of improved cultivars. Of the 20 chapters in this publication, editored by an international group of researchers, one section deals with systematics, genetics, genetic manipulation and biotic interactions of Populus, while the other deals with stress response and the physiology of growth and productivity" --

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ISBN:
Category :
Languages : en
Pages :

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Book Description
We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. Over 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event, with approximately 8,000 pairs of duplicated genes from that event surviving in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication and gross chromosomal rearrangement appear to proceed substantially slower in Populus relative to Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average between 1.4-1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with disease resistance, meristem development, metabolite transport and lignocellulosic wall biosynthesis.

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ISBN:
Category :
Languages : en
Pages :

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The goals of the S.H. Strauss laboratory portion of 'Genome-enabled discovery of carbon sequestration genes in poplar' are (1) to explore the functions of candidate genes using Populus transformation by inserting genes provided by Oakridge National Laboratory (ORNL) and the University of Florida (UF) into poplar; (2) to expand the poplar transformation toolkit by developing transformation methods for important genotypes; and (3) to allow induced expression, and efficient gene suppression, in roots and other tissues. As part of the transformation improvement effort, OSU developed transformation protocols for Populus trichocarpa 'Nisqually-1' clone and an early flowering P. alba clone, 6K10. Complete descriptions of the transformation systems were published (Ma et. al. 2004, Meilan et. al 2004). Twenty-one 'Nisqually-1' and 622 6K10 transgenic plants were generated. To identify root predominant promoters, a set of three promoters were tested for their tissue-specific expression patterns in poplar and in Arabidopsis as a model system. A novel gene, ET304, was identified by analyzing a collection of poplar enhancer trap lines generated at OSU (Filichkin et. al 2006a, 2006b). Other promoters include the pGgMT1 root-predominant promoter from Casuarina glauca and the pAtPIN2 promoter from Arabidopsis root specific PIN2 gene. OSU tested two induction systems, alcohol- and estrogen-inducible, in multiple poplar transgenics. Ethanol proved to be the more efficient when tested in tissue culture and greenhouse conditions. Two estrogen-inducible systems were evaluated in transgenic Populus, neither of which functioned reliably in tissue culture conditions. GATEWAY-compatible plant binary vectors were designed to compare the silencing efficiency of homologous (direct) RNAi vs. heterologous (transitive) RNAi inverted repeats. A set of genes was targeted for post transcriptional silencing in the model Arabidopsis system; these include the floral meristem identity gene (APETALA1 or AP1), auxin response factor gene (ETTIN), the gene encoding transcriptional factor of WD40 family (TRANSPARENTTESTAGLABRA1 or TTG1), and the auxin efflux carrier (PIN-FORMED2 or PIN2) gene. More than 220 transgenic lines of the 1st, 2nd and 3rd generations were analyzed for RNAi suppression phenotypes (Filichkin et. al., manuscript submitted). A total of 108 constructs were supplied by ORNL, UF and OSU and used to generate over 1,881 PCR verified transgenic Populus and over 300 PCR verified transgenic Arabidopsis events. The Populus transgenics alone required Agrobacterium co-cultivations of 124.406 explants.

Author: Hervé Tettelin
Publisher: Springer Nature
ISBN: 3030382818
Category : Science
Languages : en
Pages : 311

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Book Description
This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Author: Andrew Groover
Publisher: Springer
ISBN: 3319493299
Category : Science
Languages : en
Pages : 366

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Book Description
Marking the change in focus of tree genomics from single species to comparative approaches, this book covers biological, genomic, and evolutionary aspects of angiosperm trees that provide information and perspectives to support researchers broadening the focus of their research. The diversity of angiosperm trees in morphology, anatomy, physiology and biochemistry has been described and cataloged by various scientific disciplines, but the molecular, genetic, and evolutionary mechanisms underlying this diversity have only recently been explored. Excitingly, advances in genomic and sequencing technologies are ushering a new era of research broadly termed comparative genomics, which simultaneously exploits and describes the evolutionary origins and genetic regulation of traits of interest. Within tree genomics, this research is already underway, as the number of complete genome sequences available for angiosperm trees is increasing at an impressive pace and the number of species for which RNAseq data are available is rapidly expanding. Because they are extensively covered by other literature and are rapidly changing, technical and computational approaches—such as the latest sequencing technologies—are not a main focus of this book. Instead, this comprehensive volume provides a valuable, broader view of tree genomics whose relevance will outlive the particulars of current-day technical approaches. The first section of the book discusses background on the evolution and diversification of angiosperm trees, as well as offers description of the salient features and diversity of the unique physiology and wood anatomy of angiosperm trees. The second section explores the two most advanced model angiosperm tree species (poplars and eucalypts) as well as species that are soon to emerge as new models. The third section describes the structural features and evolutionary histories of angiosperm tree genomes, followed by a fourth section focusing on the genomics of traits of biological, ecological, and economic interest. In summary, this book is a timely and well-referenced foundational resource for the forest tree community looking to embrace comparative approaches for the study of angiosperm trees.

Author: Brandon Michael Brett
Publisher:
ISBN:
Category :
Languages : en
Pages : 58

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Author: Henry T. Nguyen
Publisher: Springer
ISBN: 3319641980
Category : Science
Languages : en
Pages : 211

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Book Description
This book examines the application of soybean genome sequences to comparative, structural, and functional genomics. Since the availability of the soybean genome sequence has revolutionized molecular research on this important crop species, the book also describes how the genome sequence has shaped research on transposon biology and applications for gene identification, tilling and positional gene cloning. Further, the book shows how the genome sequence influences research in the areas of genetic mapping, marker development, and genome-wide association mapping for identifying important trait genes and soybean breeding. In closing, the economic and botanical aspects of the soybean are also addressed.