NDLI: Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum

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Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum

Content Provider	PubMed Central
Author	Grativol, ClÃcia Regulski, Michael Bertalan, Marcelo Mccombie, W. Richard Silva, Felipe Rodrigues Da Neto, Adhemar Zerlotini Vicentini, Renato Farinelli, Laurent Hemerly, Adriana Silva Martienssen, Robert A. Ferreira, Paulo Cavalcanti Gomes
Abstract	Many economically important crops have large and complex genomes, which hampers sequencing of their genome by standard methods such as WGS. Large tracts of methylated repeats occur at plant genomes interspersed by hypomethylated gene-rich regions. Gene enrichment strategies based on methylation profile offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration (MF) with McrBC digestion to enrich for euchromatic regions of sugarcane genome. To verify the efficiency of MF and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using MF and unfiltered (UF) libraries. The MF allowed the achievement of a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5 times more scaffolds and 1.7 times more assembled Mb compared to unfiltered scaffolds. The coverage of sorghum CDS by MF scaffolds was at least 36% higher than by UF scaffolds. Using MF technology, we increased by 134X the coverage of genic regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds covering all genes at sugarcane BACs, 97.2% of sugarcane ESTs, 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds encoding enzymes of the sucrose/starch pathway discovered 291 SNPs in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes were also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and improvement of sugarcane as a biofuel crop.
Related Links	http://dx.doi.org/10.1111/tpj.12539
Ending Page	172
Page Count	11
Starting Page	162
File Format	PDF
ISSN	09607412
e-ISSN	1365313X
Journal	The Plant journal : for cell and molecular biology
Issue Number	1
Volume Number	79
Language	English
Publisher Date	2014-07-01
Access Restriction	Open
Subject Keyword	Plant Science Genetics Cell Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Cell Biology Genetics Plant Science

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