Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

BMC Genomics

Research Article

Luis Herrera-Estrella¹  Hamlet Avilés-Arnaut²  Gabriela Casique-Arroyo²  John P Délano-Frier²  Norma A Martínez-Gallardo²  Kena Casarrubias-Castillo²  Paula A Castrillón-Arbeláez²  Erandi Vargas-Ortiz²  Julio Massange-Sánchez²  Fannie I Parra-Cota²  María G Estrada-Hernández³ 

[1] Laboratorio Nacional de Génomica para la Biodiversidad, Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto., México;Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto., México;Unidad de Biotecnología e Ingeniería Genética de Plantas, (Cinvestav-Unidad Irapuato) Km 9.6 del Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, C.P. 36821, Irapuato, Gto., México;Department of Entomology, College of Agricultural Sciences, Penn State University, 16802, University Park, PA, USA;

关键词: Bacterial Artificial Chromosome;    Amaranth;    Insect Herbivory;    Vacuolar Processing Enzyme;    Amaranth Species;   

DOI  :  10.1186/1471-2164-12-363

 received in 2011-04-06, accepted in 2011-07-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundAmaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth.ResultsA total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa).ConclusionsThis study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.

【 授权许可】

CC BY   
© Délano-Frier et al; licensee BioMed Central Ltd. 2011