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Al‐Dossary O, Alsubaie B, Kharabian‐Masouleh A, Al‐Mssallem I, Furtado A, Henry RJ. The jojoba genome reveals wide divergence of the sex chromosomes in a dioecious plant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1283-1294. [PMID: 34570389 PMCID: PMC9293028 DOI: 10.1111/tpj.15509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Most flowering plants are hermaphrodites, but around 6% of species are dioecious, having separate male and female plants. Sex chromosomes and some sex-specific genes have been reported in plants, but the genome sequences have not been compared. We now report the genome sequence of male and female jojoba (Simmondsia chinensis) plants, revealing a very large difference in the sex chromosomes. The male genome assembly was 832 Mb and the female 822 Mb. This was explained by the large size differences in the Y chromosome (37.6 Mb) compared with the X chromosome (26.9 Mb). Relative to the X chromosome, the Y chromosome had two large insertions each of more than 5 Mb containing more than 400 genes. Many of the genes in the chromosome-specific regions were novel. These male-specific regions included many flowering-related and stress response genes. Smaller insertions found only in the X chromosome totalled 877 kb. The wide divergence of the sex chromosomes suggests a long period of adaptation to diverging sex-specific roles. Male and female plants may have evolved to accommodate factors such as differing reproductive resource allocation requirements under the stress of the desert environment in which the plants are found. The sex-determining regions accumulate genes beneficial to each sex. This has required the evolution of many more novel sex-specific genes than has been reported for other organisms. This suggest that dioecious plants provide a novel source of genes for manipulation of reproductive performance and environmental adaptation in crops.
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Affiliation(s)
- Othman Al‐Dossary
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | | | - Ibrahim Al‐Mssallem
- College of Agriculture and Food SciencesKing Faisal UniversityAl Hofuf36362Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbane4072Australia
- ARC Centre of Excellence for Plant Success in Nature and AgricultureUniversity of QueenslandBrisbane4072Australia
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2
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Grigorev K, Kliver S, Dobrynin P, Komissarov A, Wolfsberger W, Krasheninnikova K, Afanador-Hernández YM, Brandt AL, Paulino LA, Carreras R, Rodríguez LE, Núñez A, Brandt JR, Silva F, Hernández-Martich JD, Majeske AJ, Antunes A, Roca AL, O'Brien SJ, Martínez-Cruzado JC, Oleksyk TK. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. Gigascience 2018; 7:4931057. [PMID: 29718205 PMCID: PMC6009670 DOI: 10.1093/gigascience/giy025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/26/2018] [Accepted: 03/07/2018] [Indexed: 11/25/2022] Open
Abstract
Solenodons are insectivores that live in Hispaniola and Cuba. They form an isolated branch in the tree of placental mammals that are highly divergent from other eulipothyplan insectivores The history, unique biology, and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data. However, a whole genome assembly for solenodons has not been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation and reduced numbers have likely resulted in high homozygosity within the Hispaniolan solenodon (Solenodon paradoxus). Thus, we tested the performance of several assembly strategies on the genome of this genetically impoverished species. The string graph-based assembly strategy seemed a better choice compared to the conventional de Bruijn graph approach due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of 5 individuals from the southern subspecies (S. p. woodi). In addition, we obtained an additional sequence from 1 sample of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other and annotated for genes, with an emphasis on venom genes, repeats, variable microsatellite loci, and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single-copy orthologs from 10 other mammals. We estimated that solenodons diverged from other extant mammals 73.6 million years ago. Patterns of single-nucleotide polymorphism variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 thousand years ago.
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Affiliation(s)
- Kirill Grigorev
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Sergey Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Walter Wolfsberger
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | | | - Adam L Brandt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Natural Sciences, St. Norbert College, De Pere, Wisconsin, USA
| | - Liz A Paulino
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Rosanna Carreras
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Luis E Rodríguez
- Instituto Tecnológico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
| | - Adrell Núñez
- Department of Conservation and Science, Parque Zoologico Nacional (ZOODOM), Santo Domingo, Dominican Republic
| | - Jessica R Brandt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Biology, Marian University, Fond du Lac, Wisconsin, USA
| | - Filipe Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - J David Hernández-Martich
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo, Dominican Republic
| | - Audrey J Majeske
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, USA
| | | | - Taras K Oleksyk
- Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
- Biology Department, Uzhhorod National University, Uzhhorod, Ukraine
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3
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Guo W, Mishra S, Zhao J, Tang J, Zeng B, Kong F, Ning R, Li M, Zhang H, Zeng Y, Tian Y, Zhong Y, Luo H, Liu Y, Yang J, Yang M, Zhang M, Li Y, Ni Q, Li C, Wang C, Li D, Zhang H, Zuo Z, Li Y. Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda ( Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation. Front Microbiol 2018; 9:229. [PMID: 29503636 PMCID: PMC5820910 DOI: 10.3389/fmicb.2018.00229] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.
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Affiliation(s)
- Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Jingsi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Miao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hengzhi Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yutian Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yuanliangzi Tian
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yihang Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Hongdi Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yunhan Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Jiandong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Caiwu Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Zhili Zuo
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Cannarozzi G, Plaza-Wüthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blösch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014; 15:581. [PMID: 25007843 PMCID: PMC4119204 DOI: 10.1186/1471-2164-15-581] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Tef (Eragrostis tef), an indigenous cereal critical to food security in the Horn of Africa, is rich in minerals and protein, resistant to many biotic and abiotic stresses and safe for diabetics as well as sufferers of immune reactions to wheat gluten. We present the genome of tef, the first species in the grass subfamily Chloridoideae and the first allotetraploid assembled de novo. We sequenced the tef genome for marker-assisted breeding, to shed light on the molecular mechanisms conferring tef's desirable nutritional and agronomic properties, and to make its genome publicly available as a community resource. RESULTS The draft genome contains 672 Mbp representing 87% of the genome size estimated from flow cytometry. We also sequenced two transcriptomes, one from a normalized RNA library and another from unnormalized RNASeq data. The normalized RNA library revealed around 38000 transcripts that were then annotated by the SwissProt group. The CoGe comparative genomics platform was used to compare the tef genome to other genomes, notably sorghum. Scaffolds comprising approximately half of the genome size were ordered by syntenic alignment to sorghum producing tef pseudo-chromosomes, which were sorted into A and B genomes as well as compared to the genetic map of tef. The draft genome was used to identify novel SSR markers, investigate target genes for abiotic stress resistance studies, and understand the evolution of the prolamin family of proteins that are responsible for the immune response to gluten. CONCLUSIONS It is highly plausible that breeding targets previously identified in other cereal crops will also be valuable breeding targets in tef. The draft genome and transcriptome will be of great use for identifying these targets for genetic improvement of this orphan crop that is vital for feeding 50 million people in the Horn of Africa.
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Affiliation(s)
- Gina Cannarozzi
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
| | - Sonia Plaza-Wüthrich
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Korinna Esfeld
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Stéphanie Larti
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Clinic for Parodontology, University of Bern, Freiburgstrasse 7, Bern, CH-3010 Switzerland
| | - Yi Song Wilson
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Dejene Girma
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
- />Ethiopian Institute of Agricultural Research, National Biotechnology Laboratory (Holetta), P.O. Box 2003, Addis Ababa, Ethiopia
| | - Edouard de Castro
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Solomon Chanyalew
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Regula Blösch
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Laurent Farinelli
- />Fasteris SA, Ch. du Pont-du-Centenaire 109, P.O. Box 28, Plan-les-Ouates, CH-1228 Switzerland
| | - Eric Lyons
- />School of Plant Sciences, Univerisity of Arizona, 1140 E. South Campus Drive, 303 Forbes Building, P.O. Box 210036, Tucson, AZ 85721-0036 USA
| | - Michel Schneider
- />Swiss Institute of Bioinformatics, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Laurent Falquet
- />Swiss Institute of Bioinformatics, Vital-IT, Quartier Sorge - Batiment Genopode, Lausanne, 1015 Switzerland
- />Faculty of Science, University of Fribourg, Ch. du Musée 10, Fribourg, CH-1700 Switzerland
| | - Cris Kuhlemeier
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
| | - Kebebew Assefa
- />Ethiopian Institute of Agricultural Research, Debre Zeit Agricultural Research Center, P.O. Box 32, Debre Zeit, Ethiopia
| | - Zerihun Tadele
- />Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, CH-3013 Switzerland
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Kim JH, Roh JY, Kwon DH, Kim YH, Yoon KA, Yoo S, Noh SJ, Park J, Shin EH, Park MY, Lee SH. Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis. Parasit Vectors 2014; 7:279. [PMID: 24947244 PMCID: PMC4079623 DOI: 10.1186/1756-3305-7-279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leptotrombidium pallidum and Leptotrombidium scutellare are the major vector mites for Orientia tsutsugamushi, the causative agent of scrub typhus. Before these organisms can be subjected to whole-genome sequencing, it is necessary to estimate their genome sizes to obtain basic information for establishing the strategies that should be used for genome sequencing and assembly. METHOD The genome sizes of L. pallidum and L. scutellare were estimated by a method based on quantitative real-time PCR. In addition, a k-mer analysis of the whole-genome sequences obtained through Illumina sequencing was conducted to verify the mutual compatibility and reliability of the results. RESULTS The genome sizes estimated using qPCR were 191 ± 7 Mb for L. pallidum and 262 ± 13 Mb for L. scutellare. The k-mer analysis-based genome lengths were estimated to be 175 Mb for L. pallidum and 286 Mb for L. scutellare. The estimates from these two independent methods were mutually complementary and within a similar range to those of other Acariform mites. CONCLUSIONS The estimation method based on qPCR appears to be a useful alternative when the standard methods, such as flow cytometry, are impractical. The relatively small estimated genome sizes should facilitate whole-genome analysis, which could contribute to our understanding of Arachnida genome evolution and provide key information for scrub typhus prevention and mite vector competence.
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Affiliation(s)
- Ju Hyeon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Jong Yul Roh
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Young Ho Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Kyungjae A Yoon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Seungil Yoo
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - Seung-Jae Noh
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - Junhyung Park
- Deparment of Research, Codes Division, Insilicogen, Inc, Suwon 441-813, Korea
| | - E-hyun Shin
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Mi-Yeoun Park
- Division of Medical Entomology, National Institute of Health, Osong 363-951, Korea
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
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Quail MA, Matthews L, Sims S, Lloyd C, Beasley H, Baxter SW. Genomic libraries: II. Subcloning, sequencing, and assembling large-insert genomic DNA clones. Methods Mol Biol 2012; 772:59-81. [PMID: 22065432 DOI: 10.1007/978-1-61779-228-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sequencing large insert clones to completion is useful for characterizing specific genomic regions, identifying haplotypes, and closing gaps in whole genome sequencing projects. Despite being a standard technique in molecular laboratories, DNA sequencing using the Sanger method can be highly problematic when complex secondary structures or sequence repeats are encountered in genomic clones. Here, we describe methods to isolate DNA from a large insert clone (fosmid or BAC), subclone the sample, and sequence the region to the highest industry standard. Troubleshooting solutions for sequencing difficult templates are discussed.
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Affiliation(s)
- Mike A Quail
- Sequencing Research and Development, Wellcome Trust Sanger Institute, Cambridge, UK
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Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J, Edwards D. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:768-75. [PMID: 21356002 DOI: 10.1111/j.1467-7652.2010.00587.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at http://www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.
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Affiliation(s)
- Paul J Berkman
- School of Land, Crop and Food Sciences and Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
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