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Hu G, Hovav R, Grover CE, Faigenboim-Doron A, Kadmon N, Page JT, Udall JA, Wendel JF. Evolutionary Conservation and Divergence of Gene Coexpression Networks in Gossypium (Cotton) Seeds. Genome Biol Evol 2016; 8:3765-3783. [PMID: 28062755 PMCID: PMC5585989 DOI: 10.1093/gbe/evw280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication. Network comparisons among species indicate that topologies are altered in addition to gene expression profiles, indicating that changes in transcriptomic coexpression relationships play a role in the developmental architecture of cotton seed development. The global network topology of allopolyploids, especially for domesticated G. hirsutum, resembles the network of the A-genome diploid more than that of the D-genome parent, despite its D-like phenotype in oil content. Expression modifications associated with allopolyploidy include coexpression level dominance and transgressive expression, suggesting that the transcriptomic architecture in polyploids is to some extent a modular combination of that of its progenitor genomes. Among allopolyploids, intermodular relationships are more preserved between two different wild allopolyploid species than they are between wild and domesticated forms of a cultivated cotton, and regulatory connections of oil synthesis-related pathways are denser and more closely clustered in domesticated vs. wild G. hirsutum. These results demonstrate substantial modification of genic coexpression under domestication. Our work demonstrates how network inference informs our understanding of the transcriptomic architecture of phenotypic variation associated with temporal scales ranging from thousands (domestication) to millions (speciation) of years, and by polyploidy.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | - Ran Hovav
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | - Corrinne E. Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
| | | | - Noa Kadmon
- Agricultural Research Organization (Volcani Center), Bet Dagan, Israel
| | | | | | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames
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Abstract
BACKGROUND Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer's disease (AD), have epistatic causes, requiring more sophisticated analyses to identify groups of variants which together affect phenotype. RESULTS Based on the GWAS statistical model, we developed a multi-SNP GWAS analysis to identify pairs of variants whose common occurrence signaled the Alzheimer's disease phenotype. CONCLUSIONS Despite not having sufficient data to demonstrate significance, our preliminary experimentation identified a high correlation between GRIA3 and HLA-DRB5 (an AD gene). GRIA3 has not been previously reported in association with AD, but is known to play a role in learning and memory.
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Affiliation(s)
- Paul M Bodily
- Computer Science Department, Brigham Young University, Provo, 84602-6576, UT, USA.
| | - M Stanley Fujimoto
- Computer Science Department, Brigham Young University, Provo, 84602-6576, UT, USA
| | - Justin T Page
- Department of Biology, Brigham Young University, Provo, 84602-6576, UT, USA
| | - Mark J Clement
- Computer Science Department, Brigham Young University, Provo, 84602-6576, UT, USA
| | - Mark T W Ebbert
- Department of Biology, Brigham Young University, Provo, 84602-6576, UT, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, 84602-6576, UT, USA
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Renny-Byfield S, Page JT, Udall JA, Sanders WS, Peterson DG, Arick MA, Grover CE, Wendel JF. Independent Domestication of Two Old World Cotton Species. Genome Biol Evol 2016; 8:1940-7. [PMID: 27289095 PMCID: PMC4943200 DOI: 10.1093/gbe/evw129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/16/2022] Open
Abstract
Domesticated cotton species provide raw material for the majority of the world's textile industry. Two independent domestication events have been identified in allopolyploid cotton, one in Upland cotton (Gossypium hirsutum L.) and the other to Egyptian cotton (Gossypium barbadense L.). However, two diploid cotton species, Gossypium arboreum L. and Gossypium herbaceum L., have been cultivated for several millennia, but their status as independent domesticates has long been in question. Using genome resequencing data, we estimated the global abundance of various repetitive DNAs. We demonstrate that, despite negligible divergence in genome size, the two domesticated diploid cotton species contain different, but compensatory, repeat content and have thus experienced cryptic alterations in repeat abundance despite equivalence in genome size. Evidence of independent origin is bolstered by estimates of divergence times based on molecular evolutionary analysis of f7,000 orthologous genes, for which synonymous substitution rates suggest that G. arboreum and G. herbaceum last shared a common ancestor approximately 0.4-2.5 Ma. These data are incompatible with a shared domestication history during the emergence of agriculture and lead to the conclusion that G. arboreum and G. herbaceum were each domesticated independently.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University DuPont Pioneer, Johnston, IA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University
| | - William S Sanders
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Computer Science and Engineering, Mississippi State University
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University Department of Plant and Soil Sciences, Mississippi State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University
| | - Corrinne E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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Page JT, Liechty ZS, Alexander RH, Clemons K, Hulse-Kemp AM, Ashrafi H, Van Deynze A, Stelly DM, Udall JA. DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton. PLoS Genet 2016; 12:e1006012. [PMID: 27168520 PMCID: PMC4864293 DOI: 10.1371/journal.pgen.1006012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/06/2016] [Indexed: 01/08/2023] Open
Abstract
Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the AT- and DT-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.
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Affiliation(s)
- Justin T. Page
- Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Zach S. Liechty
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Rich H. Alexander
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Kimberly Clemons
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Amanda M. Hulse-Kemp
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California-Davis, Davis, California, United States of America
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
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Clouse JW, Adhikary D, Page JT, Ramaraj T, Deyholos MK, Udall JA, Fairbanks DJ, Jellen EN, Maughan PJ. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly. Plant Genome 2016; 9. [PMID: 27898770 DOI: 10.3835/plantgenome2015.07.0062] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.
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Abstract
We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata) and Low (A. arbuscula ssp. arbuscula) sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.
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Affiliation(s)
- Mark D. Huynh
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, UT, 84606, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, United States of America
- * E-mail:
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Abstract
Genome read categorization determines the genome of origin for sequence reads from an allopolyploid organism. Different techniques have been used to perform read categorization, mostly based on homoeo-SNPs identified between extant diploid relatives of allopolyploids. We present a novel technique for read categorization implemented by the software PolyDog. We demonstrate its accuracy and improved categorization relative to other methods. We discuss the situations in which one method or another might be most appropriate.
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Abstract
Background Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results. Findings We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. Conclusions BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-829) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Justin T Page
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Abstract
BACKGROUND Massive computational power is needed to analyze the genomic data produced by next-generation sequencing, but extensive computational experience and specific knowledge of algorithms should not be necessary to run genomic analyses or interpret their results. FINDINGS We present BamBam, a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. CONCLUSIONS BamBam provides a powerful and convenient framework to analyze genome sequence data contained in BAM files.
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Affiliation(s)
- Justin T Page
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biol 2014; 14:312. [PMID: 25403726 PMCID: PMC4245742 DOI: 10.1186/s12870-014-0312-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. RESULTS Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. CONCLUSIONS The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches.
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Affiliation(s)
- Olga P Yurchenko
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Sunjung Park
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
- />Department of Biological Sciences, Center for Plant Lipid Research, University of North Texas, Denton, TX 76203 USA
| | - Daniel C Ilut
- />Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - Jay J Inmon
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Jon C Millhollon
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
| | - Zach Liechty
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Justin T Page
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Matthew A Jenks
- />Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 2650 USA
| | - Kent D Chapman
- />Department of Biological Sciences, Center for Plant Lipid Research, University of North Texas, Denton, TX 76203 USA
| | - Joshua A Udall
- />Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Michael A Gore
- />Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
| | - John M Dyer
- />USDA-ARS, US Arid-Land Agricultural Research Center, 21881 North Cardon Lane, Maricopa, AZ 85138 USA
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11
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Yurchenko OP, Park S, Ilut DC, Inmon JJ, Millhollon JC, Liechty Z, Page JT, Jenks MA, Chapman KD, Udall JA, Gore MA, Dyer JM. Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium. BMC Plant Biol 2014; 14:312. [PMID: 25403726 DOI: 10.1186/s12870-014-0312-315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 10/28/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND The majority of commercial cotton varieties planted worldwide are derived from Gossypium hirsutum, which is a naturally occurring allotetraploid produced by interspecific hybridization of A- and D-genome diploid progenitor species. While most cotton species are adapted to warm, semi-arid tropical and subtropical regions, and thus perform well in these geographical areas, cotton seedlings are sensitive to cold temperature, which can significantly reduce crop yields. One of the common biochemical responses of plants to cold temperatures is an increase in omega-3 fatty acids, which protects cellular function by maintaining membrane integrity. The purpose of our study was to identify and characterize the omega-3 fatty acid desaturase (FAD) gene family in G. hirsutum, with an emphasis on identifying omega-3 FADs involved in cold temperature adaptation. RESULTS Eleven omega-3 FAD genes were identified in G. hirsutum, and characterization of the gene family in extant A and D diploid species (G. herbaceum and G. raimondii, respectively) allowed for unambiguous genome assignment of all homoeologs in tetraploid G. hirsutum. The omega-3 FAD family of cotton includes five distinct genes, two of which encode endoplasmic reticulum-type enzymes (FAD3-1 and FAD3-2) and three that encode chloroplast-type enzymes (FAD7/8-1, FAD7/8-2, and FAD7/8-3). The FAD3-2 gene was duplicated in the A genome progenitor species after the evolutionary split from the D progenitor, but before the interspecific hybridization event that gave rise to modern tetraploid cotton. RNA-seq analysis revealed conserved, gene-specific expression patterns in various organs and cell types and semi-quantitative RT-PCR further revealed that FAD7/8-1 was specifically induced during cold temperature treatment of G. hirsutum seedlings. CONCLUSIONS The omega-3 FAD gene family in cotton was characterized at the genome-wide level in three species, showing relatively ancient establishment of the gene family prior to the split of A and D diploid progenitor species. The FAD genes are differentially expressed in various organs and cell types, including fiber, and expression of the FAD7/8-1 gene was induced by cold temperature. Collectively, these data define the genetic and functional genomic properties of this important gene family in cotton and provide a foundation for future efforts to improve cotton abiotic stress tolerance through molecular breeding approaches.
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Naoumkina M, Thyssen G, Fang DD, Hinchliffe DJ, Florane C, Yeater KM, Page JT, Udall JA. The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). PLoS One 2014; 9:e90830. [PMID: 24598808 PMCID: PMC3944810 DOI: 10.1371/journal.pone.0090830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/04/2014] [Indexed: 12/18/2022] Open
Abstract
Next generation sequencing (RNA-seq) technology was used to evaluate the effects of the Ligon lintless-2 (Li2) short fiber mutation on transcriptomes of both subgenomes of allotetraploid cotton (Gossypium hirsutum L.) as compared to its near-isogenic wild type. Sequencing was performed on 4 libraries from developing fibers of Li2 mutant and wild type near-isogenic lines at the peak of elongation followed by mapping and PolyCat categorization of RNA-seq data to the reference D5 genome (G. raimondii) for homeologous gene expression analysis. The majority of homeologous genes, 83.6% according to the reference genome, were expressed during fiber elongation. Our results revealed: 1) approximately two times more genes were induced in the AT subgenome comparing to the DT subgenome in wild type and mutant fiber; 2) the subgenome expression bias was significantly reduced in the Li2 fiber transcriptome; 3) Li2 had a significantly greater effect on the DT than on the AT subgenome. Transcriptional regulators and cell wall homeologous genes significantly affected by the Li2 mutation were reviewed in detail. This is the first report to explore the effects of a single mutation on homeologous gene expression in allotetraploid cotton. These results provide deeper insights into the evolution of allotetraploid cotton gene expression and cotton fiber development.
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Affiliation(s)
- Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Gregory Thyssen
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Doug J. Hinchliffe
- Cotton Chemistry & Utilization Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Christopher Florane
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Kathleen M. Yeater
- USDA-ARS-Southern Plains Area, College Station, Texas, United States of America
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah, United States of America
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13
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Renny-Byfield S, Gallagher JP, Grover CE, Szadkowski E, Page JT, Udall JA, Wang X, Paterson AH, Wendel JF. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biol Evol 2014; 6:559-71. [PMID: 24558256 PMCID: PMC3971588 DOI: 10.1093/gbe/evu037] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/25/2022] Open
Abstract
Whole genome duplication (WGD) is widespread in flowering plants and is a driving force in angiosperm diversification. The redundancy introduced by WGD allows the evolution of novel gene interactions and functions, although the patterns and processes of diversification are poorly understood. We identified ∼ 2,000 pairs of paralogous genes in Gossypium raimondii (cotton) resulting from an approximately 60 My old 5- to 6-fold ploidy increase. Gene expression analyses revealed that, in G. raimondii, 99.4% of the gene pairs exhibit differential expression in at least one of the three tissues (petal, leaf, and seed), with 93% to 94% exhibiting differential expression on a per-tissue basis. For 1,666 (85%) pairs, differential expression was observed in all tissues. These observations were mirrored in a time series of G. raimondii seed, and separately in leaf, petal, and seed of G. arboreum, indicating expression level diversification before species divergence. A generalized linear model revealed 92.4% of the paralog pairs exhibited expression divergence, with most exhibiting significant gene and tissue interactions indicating complementary expression patterns in different tissues. These data indicate massive, near-complete expression level neo- and/or subfunctionalization among ancient gene duplicates, suggesting these processes are essential in their maintenance over ∼ 60 Ma.
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Affiliation(s)
- Simon Renny-Byfield
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Joseph P. Gallagher
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Corrinne E. Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Emmanuel Szadkowski
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
| | - Justin T. Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, Utah
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia
| | | | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
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14
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Abstract
Background Genes duplicated by polyploidy (homoeologs) may be differentially expressed in plant tissues. Recent research using DNA microarrays and RNAseq data have described a cacophony of complex expression patterns during development of cotton fibers, petals, and leaves. Because of its highly canalized development, petal tissue has been used as a model tissue for gene expression in cotton. Recent advances in cotton genome annotation and assembly now permit an enhanced analysis of duplicate gene deployment in petals from allopolyploid cotton. Results Homoeologous gene expression levels were quantified in diploid and tetraploid flower petals of Gossypium using the Gossypium raimondii genome sequence as a reference. In the polyploid, most homoeologous genes were expressed at equal levels, though a subset had an expression bias of AT and DT copies. The direction of gene expression bias was conserved in natural and recent polyploids of cotton. Conservation of direction of bias and additional comparisons between the diploids and tetraploids suggested different regulation mechanisms of gene expression. We described three phases in the evolution of cotton genomes that contribute to gene expression in the polyploid nucleus. Conclusions Compared to previous studies, a surprising level of expression homeostasis was observed in the expression patterns of polyploid genomes. Conserved expression bias in polyploid petals may have resulted from cis-acting modifications that occurred prior to polyploidization. Some duplicated genes were intriguing exceptions to general trends. Mechanisms of gene regulation for these and other genes in the cotton genome warrants further investigation.
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Affiliation(s)
- Aditi Rambani
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Justin T Page
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
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Bowman MJ, Park W, Bauer PJ, Udall JA, Page JT, Raney J, Scheffler BE, Jones DC, Campbell BT. RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress. PLoS One 2013; 8:e82634. [PMID: 24324815 PMCID: PMC3855774 DOI: 10.1371/journal.pone.0082634] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
An RNA-Seq experiment was performed using field grown well-watered and naturally rain fed cotton plants to identify differentially expressed transcripts under water-deficit stress. Our work constitutes the first application of the newly published diploid D5 Gossypium raimondii sequence in the study of tetraploid AD1 upland cotton RNA-seq transcriptome analysis. A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed root tissues, in patterns that confirm the accuracy of this technique for future studies in cotton genomics. Additionally, putative sequence based genome localization of differentially expressed transcripts detected A2 genome specific gene expression under water-deficit stress. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.
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Affiliation(s)
- Megan J. Bowman
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Wonkeun Park
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
- Clemson University Pee Dee Research and Education Center, Florence, South Carolina, United States of America
| | - Philip J. Bauer
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
| | - Joshua A. Udall
- Brigham Young University, Provo, Utah, United States of America
| | - Justin T. Page
- Brigham Young University, Provo, Utah, United States of America
| | - Joshua Raney
- Brigham Young University, Provo, Utah, United States of America
| | | | - Don. C. Jones
- Cotton Incorporated, Agricultural and Environmental Research, Cary, North Carolina, United States of America
| | - B. Todd Campbell
- USDA-ARS, Coastal Plains Soil, Water and Plant Research Center, Florence, South Carolina, United States of America
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Page JT. [Health policy and legislation concerning traditional indigenous medicine in Mexico]. CAD SAUDE PUBLICA 1995; 11:202-11. [PMID: 14528327 DOI: 10.1590/s0102-311x1995000200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Various Mexican federal and state government agencies dealing with indigenous affairs are trying to establish control over traditional medicine and by recognizing it achieve cost decreases for health care directed towards Indian groups, bolstering it as a first-care level. The result is that the community absorbs the costs of medical care, leading to a reduction in the number of patients seeking government-run health care services. Traditional indigenous healers and their organizations consider the law a two-edged sword. On the one hand it provides them with legal measures for their protection, but on the other, they perceive it as a dangerous threat to their culture and practices. This has led them to seek legal advice, training, and active participation in the drafting process for such legislation. The result of this project is that they have been able to learn about the law, discuss their demands, and work out a proposal which is included in this document.
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Affiliation(s)
- J T Page
- Instituto de Estudios Indígenas, Universidad Autónoma de Chiapas, San Cristóbal de las Casas, Chiapas, 29200, México
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