NDLI: 454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust

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454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust

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454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust

Content Provider	ACM Digital Library
Author	Shotland, Yoram
Abstract	Over the past few years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over five orders of magnitude. We used two of these methods to reveal the genome sequence of a highly abundant cyanobacterium in biological desert crust. These new rapid evolved next-generation sequencing technologies posed challenges for us, the bioinformatics, in terms of sequence quality scoring, alignment, assembly and more, making de novo assembly, a challenge. We are working on solving the genome of a desert cyanobacterium from biological sand crusts. Biological sand crusts are found in many deserts around the world. They play an important role in stabilizing sandy areas and affect the vegetation composition. The crusts are formed by adhesion of the sand to extracellular polysaccharides excreted mainly by filamentous cyanobacteria. Their destruction by man-made activities is considered an important promoter of desertification. Using the SOLiD™ System, we were able to get most of the genes in the genome; however, the short reads, produce by the SOLiD™ technique, assembled into short contigs, which failed to assemble into scaffolds and the draft output was highly fragmented. By combining an addition sequencing method, the 454, we were able to get much longer contigs, which assembled into scaffolds. However the 454 method introduced sequence contamination. The fragmented SOLiD™ data helped us to filter out these sequence contaminants. Only the combination of the two methods enabled us to produce the pure draft genome.
Starting Page	510
Ending Page	512
Page Count	3
File Format	PDF
ISBN	9781450316705
DOI	10.1145/2382936.2383003
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2012-10-07
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Genomic analysis Next generation dna sequencing Genomic assembly Genome comparison
Content Type	Text
Resource Type	Article

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