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Iowa State University

Plant Sciences

Ecology, Evolution and Organismal Biology Publications

Cotton

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The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel Nov 2019

The Genome Sequence Of Gossypioides Kirkii Illustrates A Descending Dysploidy In Plants, Joshua A. Udall, Evan Long, Thiruvarangan Ramaraj, Justin L. Conover, Daojun Yuan, Corrinne E. Grover, Lei Gong, Mark A. Arick Ii, Rick E. Masonbrink, Daniel G. Peterson, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome number of 13. The two exceptions are sister genera that have n = 12 (the Hawaiian Kokia and the East African and Madagascan Gossypioides). We generated a high-quality genome sequence of Gossypioides kirkii (n = 12) using PacBio, Bionano, and Hi-C technologies, and compared this assembly to genome sequences of Kokia (n = 12) and Gossypium diploids (n = 13). Previous analysis demonstrated that ...


Diversity Analysis Of Cotton (Gossypium Hirsutum L.) Germplasm Using The Cottonsnp63k Array, Jonathan F. Wendel, Lori L. Hinze, Amanda M. Hulse-Kemp, Iain W. Wilson, Qian-Hao Zhu, Danny J. Llewellyn, Jen M. Taylor, Andrew Spriggs, David D. Fang, Mauricio Ulloa, John J. Burke, Marc Giband, Jean-Marc Lacape, Allen Van Deynze, Joshua A. Udall, Jodi A. Scheffler, Steve Hague, Alan E. Pepper, James Frelichowski, Cindy T. Lawley, Don C. Jones, Richard G. Percy, David M. Stelly Jan 2017

Diversity Analysis Of Cotton (Gossypium Hirsutum L.) Germplasm Using The Cottonsnp63k Array, Jonathan F. Wendel, Lori L. Hinze, Amanda M. Hulse-Kemp, Iain W. Wilson, Qian-Hao Zhu, Danny J. Llewellyn, Jen M. Taylor, Andrew Spriggs, David D. Fang, Mauricio Ulloa, John J. Burke, Marc Giband, Jean-Marc Lacape, Allen Van Deynze, Joshua A. Udall, Jodi A. Scheffler, Steve Hague, Alan E. Pepper, James Frelichowski, Cindy T. Lawley, Don C. Jones, Richard G. Percy, David M. Stelly

Ecology, Evolution and Organismal Biology Publications

Background

Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient ...


Duplicate Gene Revolution, Homoeologous Recombination, And Transcriptome Characterization In Allopolyploid Cotton, Lex E. Flagel, Jonathan F. Wendel, Joshua A. Udall Jul 2012

Duplicate Gene Revolution, Homoeologous Recombination, And Transcriptome Characterization In Allopolyploid Cotton, Lex E. Flagel, Jonathan F. Wendel, Joshua A. Udall

Ecology, Evolution and Organismal Biology Publications

Modern allotetraploid cotton contains an “A” and “D” genome from an ancestral polyploidy event that occurred approximately 1–2 million years ago. Diploid A- and D-genome species can be compared to the A- and D-genomes found within these allotetraploids to make evolutionary inferences about polyploidy. In this paper we present a comprehensive EST assembly derived from diploid and model allotetraploid cottons and demonstrate several evolutionary inferences regarding genic evolution that can be drawn from these data. We generated a set of cotton expressed sequence tags (ESTs), comprising approximately 4.4 million Sanger and next-generation (454) transcripts supplemented by approximately 152 ...


Initiation And Early Development Of Fiber In Wild And Cultivated Cotton, Kara M. Butterworth, Dean C. Adams, Harry T. Horner, Jonathan F. Wendel Jun 2009

Initiation And Early Development Of Fiber In Wild And Cultivated Cotton, Kara M. Butterworth, Dean C. Adams, Harry T. Horner, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Cultivated cotton fiber has undergone transformation from short, coarse fibers found in progenitor wild species to economically important, long, fine fibers grown globally. Morphological transformation requires understanding of development of wild fiber and developmental differences between wild and cultivated fiber.We examined early development of fibers, including abundance and placement on seed surface, nucleus position, presence of vacuoles, and fiber size and shape. Four species were studied using microscopic, morphometric, and statistical methods: Gossypium raimondii (wild D genome), Gossypium herbaceum (cultivated A genome), Gossypium hirsutum (wild tetraploid), and Gossypium hirsutum (cultivated tetraploid). Early fiber development is highly asynchronous in G ...


Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel Apr 2008

Duplicate Gene Expression In Allopolyploid Gossypium Reveals Two Temporally Distinct Phases Of Expression Evolution, Lex E. Flagel, Joshua A. Udall, Dan Nettleton, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on duplicate genes. We compared homoeolog (genes duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 ...


The Evolution Of Spinnable Cotton Fiber Entailed Prolonged Development And A Novel Metabolism, Ran Hovav, Joshua A. Udall, Bhupendra Chaudhary, Einat Hovav, Lex Flagel, Guanjing Hu, Jonathan F. Wendel Feb 2008

The Evolution Of Spinnable Cotton Fiber Entailed Prolonged Development And A Novel Metabolism, Ran Hovav, Joshua A. Udall, Bhupendra Chaudhary, Einat Hovav, Lex Flagel, Guanjing Hu, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

A central question in evolutionary biology concerns the developmental processes by which new phenotypes arise. An exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium (‘‘cotton fiber’’). We have used fiber development in Gossypium as a system to understand how morphology can rapidly evolve. Fiber has undergone considerable morphological changes between the short, tightly adherent fibers of G. longicalyx and the derived long, spinnable fibers of its closest relative, G. herbaceum, which facilitated cotton domestication. We conducted comparative gene expression profiling across a developmental time-course of fibers from G. longicalyx and G. herbaceum using microarrays with ;22 ...


Toward Sequencing Cotton (Gossypium) Genomes, Z. Jeffrey Chen, Brian Eric Scheffler, Elizabeth Dennis, Barbara A. Triplett, Tianzhen Zhang, Wangzhen Guo, Xiaoya Chen, David M. Stelly, Pablo D. Rabinowicz, Christopher D. Town, Tony Arioli, Curt Brubaker, Roy G. Cantrell, Jean-Marc Lacape, Mauricio Ulloa, Peng Chee, Candace Haigler, Richard G. Percy, Alan R. Gingle, Sukumar Saha, Thea Wilkins, Robert J. Wright, Allen Van Deynze, Yuxian Zhu, Shuxun Yu, Ibrokhim Abdurakhmonov, P. Ananda Kumar, Mehboob-Ur- Rahman, Yusuf Zafar, John Z. Yu, Russell J. Ohel, Jonathan F. Wendel, Andrew H. Paterson Dec 2007

Toward Sequencing Cotton (Gossypium) Genomes, Z. Jeffrey Chen, Brian Eric Scheffler, Elizabeth Dennis, Barbara A. Triplett, Tianzhen Zhang, Wangzhen Guo, Xiaoya Chen, David M. Stelly, Pablo D. Rabinowicz, Christopher D. Town, Tony Arioli, Curt Brubaker, Roy G. Cantrell, Jean-Marc Lacape, Mauricio Ulloa, Peng Chee, Candace Haigler, Richard G. Percy, Alan R. Gingle, Sukumar Saha, Thea Wilkins, Robert J. Wright, Allen Van Deynze, Yuxian Zhu, Shuxun Yu, Ibrokhim Abdurakhmonov, P. Ananda Kumar, Mehboob-Ur- Rahman, Yusuf Zafar, John Z. Yu, Russell J. Ohel, Jonathan F. Wendel, Andrew H. Paterson

Ecology, Evolution and Organismal Biology Publications

Despite rapidly decreasing costs and innovative technologies, sequencing of angiosperm genomes is not yet undertaken lightly. Generating larger amounts of sequence data more quickly does not address the difficulties of sequencing and assembling complex genomes de novo. The cotton (Gossypium spp.) genomes represent a challenging case. To this end, a coalition of cotton genome scientists has developed a strategy for sequencing the cotton genomes, which will vastly expand opportunities for cotton research and improvement worldwide.


Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel Jan 2007

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to ...


Differential Lineage-Specific Amplification Of Transposable Elements Is Responsible For Genome Size Variation In Gossypium, Jennifer S. Hawkins, Hyeran Kim, John D. Nason, Rod A. Wing, Jonathan F. Wendel Oct 2006

Differential Lineage-Specific Amplification Of Transposable Elements Is Responsible For Genome Size Variation In Gossypium, Jennifer S. Hawkins, Hyeran Kim, John D. Nason, Rod A. Wing, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

The DNA content of eukaryotic nuclei (C-value) varies ∼200,000-fold, but there is only a ∼20-fold variation in the number of protein-coding genes. Hence, most C-value variation is ascribed to the repetitive fraction, although little is known about the evolutionary dynamics of the specific components that lead to genome size variation. To understand the modes and mechanisms that underlie variation in genome composition, we generated sequence data from whole genome shotgun (WGS) libraries for three representative diploid (n = 13) members of Gossypium that vary in genome size from 880 to 2460 Mb (1C) and from a phylogenetic outgroup, Gossypioides kirkii ...


A Global Assembly Of Cotton Ests, Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael Edward Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Catriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Yin Ying Guo, Xiao Ya Chen, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen Mcfadden, Paxton Payton, Natalya Klueva, Randell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, Hyeran Kim, Danny J. Llewellyn, Elizabeth S. Dennis, Rod Wing, Andrew H. Paterson, Cari Soderlund, Jonathan F. Wendel Feb 2006

A Global Assembly Of Cotton Ests, Joshua A. Udall, Jordan M. Swanson, Karl Haller, Ryan A. Rapp, Michael Edward Sparks, Jamie Hatfield, Yeisoo Yu, Yingru Wu, Catriona Dowd, Aladdin B. Arpat, Brad A. Sickler, Thea A. Wilkins, Yin Ying Guo, Xiao Ya Chen, Jodi Scheffler, Earl Taliercio, Ricky Turley, Helen Mcfadden, Paxton Payton, Natalya Klueva, Randell Allen, Deshui Zhang, Candace Haigler, Curtis Wilkerson, Jinfeng Suo, Stefan R. Schulze, Margaret L. Pierce, Margaret Essenberg, Hyeran Kim, Danny J. Llewellyn, Elizabeth S. Dennis, Rod Wing, Andrew H. Paterson, Cari Soderlund, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; AT and DT genomes) as well as its two diploid progenitors,Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to ...


Phylogeny Of The New World Diploid Cottons (Gossypium L., Malvaceae) Based On Sequences Of Three Low-Copy Nuclear Genes, Inés Álvarez, Richard Clark Cronn, Jonathan F. Wendel May 2005

Phylogeny Of The New World Diploid Cottons (Gossypium L., Malvaceae) Based On Sequences Of Three Low-Copy Nuclear Genes, Inés Álvarez, Richard Clark Cronn, Jonathan F. Wendel

Ecology, Evolution and Organismal Biology Publications

American diploid cottons (Gossypium L., subgenus Houzingenia Fryxell) form a monophyletic group of 13 species distributed mainly in western Mexico, extending into Arizona, Baja California, and with one disjunct species each in the Galapagos Islands and Peru. Prior phylogenetic analyses based on an alcohol dehydrogenase gene (AdhA) and nuclear ribosomal DNA indicated the need for additional data from other molecular markers to resolve phylogenetic relationships within this subgenus. Toward this end, we sequenced three nuclear genes, the anonymous locus A1341, an alcohol dehydrogenase gene (AdhC), and a cellulose synthase gene (CesA1b). Independent and combined analyses resolved clades ...