ena-STUDY-ARO-VOLC-11-06-2013-09:26:53:588-321
Transcriptional profiling of sweetpotato (Ipomoea batatas) roots indicates down-regulation of lignin biosynthesis and up-regulation of starch biosynthesis at an early stage of storage root formation.
The number of fibrous roots that will develop into storage roots determine sweetpotato yield. The aim of the present study was the identification of molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) Generating a database of sweetpotato root transcriptome, using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous- and initiating storage-roots (2) Comparing the expression profiles of initiating storage roots and fibrous roots using the Illumina Genome Analyser, for sequencing cDNA libraries of the two root types and mapping the data onto the root transcriptome database.  Use of the 454-Roche platform generated a total of 524,607 reads, of which 85.6% were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyser, were found to map to 31,284 contigs out of the 55,296 contigs that served as a database. A total of 8,474 contigs were found to exhibit differential expression between the two root types (fold-change being at least 2.5). The Illumina-based differential expression results were validated for 9 putative genes using quantitative real-time PCR. The differential expression profiles indicate down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, the data indicate a delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.  This study adds a valuable resource of sweetpotato root transcript sequences to the available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow towards phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel storage-root-initiation-related transcripts identified in this study provide a good start for further investigation into the molecular mechanisms underlying this process.
The number of fibrous roots that will develop into storage roots determine sweetpotato yield. The aim of the present study was the identification of molecular mechanisms involved in the initiation of storage root formation, by performing a detailed transcriptomic analysis of initiating storage roots using next-generation sequencing platforms. A two-step approach was undertaken: (1) Generating a database of sweetpotato root transcriptome, using 454-Roche sequencing of a cDNA library created from pooled samples of two root types: fibrous- and initiating storage-roots (2) Comparing the expression profiles of initiating storage roots and fibrous roots using the Illumina Genome Analyser, for sequencing cDNA libraries of the two root types and mapping the data onto the root transcriptome database.  Use of the 454-Roche platform generated a total of 524,607 reads, of which 85.6% were clustered into 55,296 contigs that matched 40,278 known genes. The reads, generated by the Illumina Genome Analyser, were found to map to 31,284 contigs out of the 55,296 contigs that served as a database. A total of 8,474 contigs were found to exhibit differential expression between the two root types (fold-change being at least 2.5). The Illumina-based differential expression results were validated for 9 putative genes using quantitative real-time PCR. The differential expression profiles indicate down-regulation of classical root functions, such as transport, as well as down-regulation of lignin biosynthesis in initiating storage roots and up-regulation of carbohydrate metabolism and starch biosynthesis. In addition, the data indicate a delicate control of regulators of meristematic tissue identity and maintenance, associated with the initiation of storage root formation.  This study adds a valuable resource of sweetpotato root transcript sequences to the available data, facilitating the identification of genes of interest. This resource enabled us to identify genes that are involved in the earliest stage of storage root formation, highlighting the reduction in carbon flow towards phenylpropanoid biosynthesis and its delivery into carbohydrate metabolism and starch biosynthesis, as major events involved in storage root initiation. The novel storage-root-initiation-related transcripts identified in this study provide a good start for further investigation into the molecular mechanisms underlying this process.