Sequencing Customers Making Significant Discoveries in Plant Science
1A team led researchers at the Minzu University of China highlight the utility of high-throughput transcriptome sequencing as a fast and cost-effective approach for marker development and gene discovery in non-model species.
Ammopiptanthus mongolicus is an ecologically important plant species in Mid-Asia desert and exhibits substantial tolerance to drought condition. Insufficient transcriptomic and genomic data in public databases has limited our understanding of the molecular mechanism underlying the stress tolerance of A. mongolicus. They used 454 pyrosequencing to identify assembled sequences representing approximately 9,771 proteins in PlantGDB. The 29,056 unique sequences in this 454EST collection represent a major transcriptomic level resource for A. mongolicus, and will be useful for further functional genomics study in Ammopiptanthus genus. The thousands of SSR markers predicted in our 454 ESTs should facilitate population genomic studies in Ammopiptanthus. The potential drought stress related transcripts identified in this study provide a good start for further investigation into the drought adaptation in Ammopiptanthus.
2A study led by researchers at Nanjing Agricultural University, China provides the first small RNA expression analysis throughout the entire grain filling phase in an indica rice cultivar.
Using LC Sciences microRNA discovery and profiling services, they discovered 11 potential novel miRNAs based on the presence of their miRNA*s. A total of 21 conserved and 91 non-conserved miRNA families were found in developing indica grains. Expression patterns of these identified miRNAs were analyzed using customized miRNA chips. Their small RNA sequencing and chip analysis enlarged the rice miRNA repertoire and confirmed the existence of most conserved, and nearly half of the non-conserved, rice miRNAs in developing grains. Comparison between the three phases of grain filling revealed that these miRNAs and their targets may be involved in diverse pathways, which may also be conserved in other cereal plants. The complexity of these miRNAs and their targets and interactions require further study to obtain a better understanding of the molecular mechanisms underlying grain development.
- Zhou Y, Gao F, Liu R, Feng J, Li H, (2012) De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. BMC Genomics 13(1), 266. [article]
- Lan Y, Su N, Shen Y, Zhang R, Wu F, Cheng Z, Wang J, Zhang X, Guo X, Lei C, Wang J, Jiang L, Mao L, Wan J. (2012) Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice. BMC Genomics 13(1), 264. [Epub ahead of print]. [article]