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قابل دانلود از چهارشنبه, ۶ ارديبهشت ۱۴۰۲
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فهرست مطالب: Preface . . . . . . . . . . . . . . vAcknowledgments . . . . . . . . . . . vii Contributors . . . . . . . . . . . . . . . xiii PART I COMPARATIVE GENOMICS TO STUDY (PALEO-)POLYPLOIDY 1 Inference of Ancient Polyploidy from Genomic Data . . . . 3 Hengchi Chen and Arthur Zwaenepoel 2 Navigating the CoGe Online Software Suite for Polyploidy Research . . . . . . . . . . . . . 19 Victor A. Albert and Trevor J. Krabbenhoft 3 Inference of Ancient Polyploidy Using Transcriptome Data . . . 47 Jia Li, Yves Van de Peer, and Zhen Li 4 POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics . . 77 Gavin C. Conant 5 Applying Machine Learning to Classify the Origins of Gene Duplications . . . . . . . . . . . . 91 Michael T. W. McKibben and Michael S. Barker PART II PHYLOGENETICS TO STUDY POLYPLOIDY 6 Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach . . . . . . . . . . 123 William A. Freyman and Carl J. Rothfels 7 Constraining Whole-Genome Duplication Events in Geological Time . . . . . . . . . 139 James W. Clark and Philip C. J. Donoghue 8 SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event . . . . . . . . . . 155 Elise Parey, Hugues Roest Crollius, and Camille Berthelot 9 Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol . . . . . . . . . . 175 Anna Rice and Itay Mayrose 10 PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem . . . . . 189 Peter Schafran, Fay-Wei Li, and Carl J. Rothfels ixx Contents PART III ANALYSIS OF GENE EXPRESSION AND REGULATION IN POLYPLOIDS 11 Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model . . . . . . . 209 Ksenia Arzumanova, Rori V. Rohlfs, Lars Grønvold, Marius A. Strand, Torgeir R. Hvidsten, and Simen R. Sandve 12 Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq . . 227 Jeremy E. Coate 13 A Robust Methodology for Assessing Homoeolog-Specific Expression . . . . . . . . . . . 251 J. Lucas Boatwright PART IV POPULATION GENOMICS APPROACHES TO STUDY POLYPLOIDY 14 Analyzing Autopolyploid Genetic Data Using GenoDive . . . . . 261 Patrick G. Meirmans 15 Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data . . . . . . . . . . . . . 279 Alison Dawn Scott, Jozefien D. Van de Velde, and Polina Yu Novikova 16 Population Genomic Analysis of Diploid-Autopolyploid Species . . . . 297 Magdalena Bohutı´nska´, Jakub Vlcˇek, Patrick Monnahan, and Filip Kola´rˇ 17 Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC . . . . . . . . . . . 325 Camille Roux, Xavier Vekemans, and John Pannell PART V EXPERIMENTAL APPROACHES TO STUDY POLYPLOIDY 18 Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas . . . . . . . . . 351 Quinten Bafort, Lucas Prost, Eylem Aydogdu, Antoine Van de Vloet, Griet Casteleyn, Yves Van de Peer, and Olivier De Clerck 19 Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza . . . . . . . . . . . . 373 Tian Wu, Annelore Natran, Lucas Prost, Eylem Aydogdu, Yves Van de Peer, and Quinten Bafort 20 Experimental Approaches to Generate and Isolate Human Tetraploid Cells . . . . . . . . . . . . 391 Sara Vanessa Bernhard, Simon Gemble, Renata Basto, and Zuzana Storchova 21 Measuring Cellular Ploidy In Situ by Light Microscopy . . . . . . . 401 Delisa E. Clay, Benjamin M. Stormo, and Donald T. Fox 22 Using Mosaic Cell Labeling to Visualize Polyploid Cells in the Drosophila Brain . . . . . . . . . . 413 Shyama Nandakumar and Laura ButtittaContents xi PART VI SEQUENCING, ASSEMBLING, EDITING AND ENGINEERING POLYPLOID GENOMES 23 Sequencing and Assembly of Polyploid Genomes . . . . . . . 429 Yibin Wang, Jiaxin Yu, Mengwei Jiang, Wenlong Lei, Xingtan Zhang, and Haibao Tang 24 Genome Editing by CRISPR/Cas9 in Polyploids . . . . . . . 459 Carlos Sa´nchez-Gomez, David Pose´, and Carmen Martı´n-Pizarro 25 Developing a CRISPR System in Nongenetic Model Polyploids . . . . 475 Shengchen Shan, Bing Yang, Bernard A. Hauser, Pamela S. Soltis, and Douglas E. Soltis 26 Efficiently Editing Multiple Duplicated Homeologs and Alleles for Recurrent Polyploids . . . . . . . . . 491 Rui-Hai Gan, Li Zhou, and Jian-Fang Gui Index . . . . . . . . . . . . . . . 513 مشخصات فایل |
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| عنوان (Title): | Polyploidy_ Methods and Protocols |
| نام فایل (File name): | 943-www.GeneProtocols.ir-Polyploidy_ Methods and Protocols-Humana Press (2023).pdf |
| عنوان فارسی (Title in Persian): | پلی پلوئیدی - روشها و پروتکل ها |
| ایجاد کننده: | Yves Van de Peer |
| زبان (Language): | انگلیسی English |
| سال انتشار: | 2023 |
| شابک ISBN: | 1071625608, 9781071625606 |
| نوع سند (Doc. type): | کتاب |
| فرمت (File extention): | |
| حجم فایل (File size): | 27.1 مگابایت |
| تعداد صفحات (Book length in pages): | 514 |
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