De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
作者： Claudio Benicio Cardoso-Silva , Estela Araujo Costa , Melina Cristina Mancini , Thiago Willian Almeida Balsalobre , Lucas Eduardo Costa Canesin
DOI: 10.1371/JOURNAL.PONE.0088462
关键词: Biology 、 Expressed sequence tag 、 Sequence assembly 、 Microsatellite 、 Gene 、 Genetics 、 Transcriptome 、 Single-nucleotide polymorphism 、 Genetic marker 、 Genotype 、 General Biochemistry, Genetics and Molecular Biology 、 General Agricultural and Biological Sciences 、 General Medicine
摘要: Sugarcane is an important crop and a major source of sugar alcohol. In this study, we performed de novo assembly transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The the was using short reads generated Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on similarity search, unigenes showed significant to 28,788 sorghum proteins, including set 5,272 that are not present public EST databases; many these likely putative undescribed genes. From collection unigenes, large number molecular markers identified, 5,106 simple sequence repeats (SSRs) 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be useful resource future genetic genomic studies species.
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L Grivet, A D'Hont, P Dufour, P Hamon, D Roques, J C Glaszmann, Comparative genome mapping of sugar cane with other species within the Andropogoneae tribe Heredity. ,vol. 73, pp. 500- 508 ,(1994) , 10.1038/HDY.1994.148
Thiago Marconi, Estela Costa, Hercilia Miranda, Melina Mancini, Claudio Cardoso-Silva, Karine Oliveira, Luciana Pinto, Marcelo Mollinari, Antonio Garcia, Anete Souza, None, Functional markers for gene mapping and genetic diversity studies in sugarcane BMC Research Notes. ,vol. 4, pp. 264- 264 ,(2011) , 10.1186/1756-0500-4-264
Olena Morozova, Marco A. Marra, Applications of next-generation sequencing technologies in functional genomics. Genomics. ,vol. 92, pp. 255- 264 ,(2008) , 10.1016/J.YGENO.2008.07.001
Candice N Hansey, Brieanne Vaillancourt, Rajandeep S Sekhon, Natalia De Leon, Shawn M Kaeppler, C Robin Buell, None, Maize (zea mays L.) genome diversity as revealed by rna-sequencing PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0033071
Pablo Cingolani, Viral M. Patel, Melissa Coon, Tung Nguyen, Susan J. Land, Douglas M. Ruden, Xiangyi Lu, Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift Frontiers in Genetics. ,vol. 3, pp. 35- 35 ,(2012) , 10.3389/FGENE.2012.00035
Aurélie Kapusta, Zev Kronenberg, Vincent J. Lynch, Xiaoyu Zhuo, LeeAnn Ramsay, Guillaume Bourque, Mark Yandell, Cédric Feschotte, Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs PLoS Genetics. ,vol. 9, pp. e1003470- ,(2013) , 10.1371/JOURNAL.PGEN.1003470
D. Carson, F. Botha, Genes expressed in sugarcane maturing internodal tissue Plant Cell Reports. ,vol. 20, pp. 1075- 1081 ,(2002) , 10.1007/S00299-002-0444-1
Peter Clote, Fabrizio Ferré, Evangelos Kranakis, Danny Krizanc, Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency RNA. ,vol. 11, pp. 578- 591 ,(2005) , 10.1261/RNA.7220505
Neil I. Bower, Rosanne E. Casu, Donald J. Maclean, Antonio Reverter, Scott C. Chapman, John M. Manners, Transcriptional response of sugarcane roots to methyl jasmonate Plant Science. ,vol. 168, pp. 761- 772 ,(2005) , 10.1016/J.PLANTSCI.2004.10.006
Mingying Liu, Guirong Qiao, Jing Jiang, Huiqin Yang, Lihua Xie, Jinzhong Xie, Renying Zhuo, Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform PLoS ONE. ,vol. 7, pp. e46766- ,(2012) , 10.1371/JOURNAL.PONE.0046766