The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery
Open accessAbstract
Background: Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results: Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 10 6 expressed sequence tags (ESTs). De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR)-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions: A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.
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Cites
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
VERA, J. C., WHEAT, C. W., FESCEMYER, H. W., FRILANDER, M. J., CRAWFORD, D. L., HANSKI, I., & MARDEN, J. H. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03666.x · Cited by 714 · cited 1×
“Some recent studies have indicated that short reads from 454 GS FLX pyrosequencing may be effectively assembled and used to characterise the gene space in various organisms [16,21,32,33].”
BackgroundSequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479
Parchman, T. L., Geist, K. S., Grahnen, J. A., Benkman, C. W., & Buerkle, C. A. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-180 · Cited by 446
SNP discovery via 454 transcriptome sequencing
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Sun, C., Li, Y., Wu, Q., Luo, H., Sun, Y., Song, J., Lui, E. M., & Chen, S. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-262 · Cited by 286
Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing
Wang, W., Wang, Y., Zhang, Q., Qi, Y., & Guo, D. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-465 · Cited by 224
The Arabidopsis genome: A foundation for plant research
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Cited by
The Legume Phylogeny Working Group, Bruneau, A., Doyle, J. J., Herendeen, P., Hughes, C., Kenicer, G., Lewis, G., Mackinder, B., Pennington, R. T., Sanderson, M. J., et al. (2013) · TAXON · doi:10.12705/622.8 · Cited by 437
Metadata
- Authors
- Kaur, S., Cogan, N. O., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., & Forster, J. W.
- Venue
- BMC Genomics
- Published
- 2011-05-25
- Volume
- 12
- Issue
- 1
- Pages
- 265-265
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W1978950685
- Cited by
- 200
- References
- 8
- FWCI
- 25.79
- Type
- journal article
- Language
- en
- Open access
- gold
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- Kaur, S., Cogan, N. O., Pembleton, L. W., Shinozuka, M., Savin, K. W., Materne, M., & Forster, J. W. (2011). Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery. BMC Genomics. https://doi.org/10.1186/1471-2164-12-265
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