Ontology highlight
ABSTRACT:
PROVIDER: PRJNA628807 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11621960_1.fastq.gz | Fastqsanger.gz | |||
| SRR11621960_2.fastq.gz | Fastqsanger.gz | |||
| SRR11621961_1.fastq.gz | Fastqsanger.gz | |||
| SRR11621961_2.fastq.gz | Fastqsanger.gz | |||
| SRR11621962_1.fastq.gz | Fastqsanger.gz |
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Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock. Examination of 2 different tissue types at different developmental stages (Elongating vs. post-elongation stem internodes) in two alfalfa genotypes (708 and 773) with divergent cell wall composition in stems.
2011-04-21 | E-GEOD-26757 | biostudies-arrayexpress
Project description:Alfalfa, [Medicago sativa (L.) sativa], a widely-grown perennial forage has potential for development as a cellulosic ethanol feedstock. The application of genomic approaches would advance development of alfalfa as a cellulosic feedstock. However, the genomics of alfalfa, a non-model species, is still in its infancy. The recent advent of RNA-Seq, a massively parallel sequencing method for transcriptome analysis, provides an opportunity to expand the identification of alfalfa genes and polymorphisms, and conduct in-depth transcript profiling. Cell walls in stems of alfalfa genotype 708 have higher cellulose and lower lignin concentrations compared to cell walls in stems of genotype 773. Using the Illumina GA-II platform, a total of 198,861,304 expression sequence tags (ESTs, 76 bp in length) were generated from cDNA libraries derived from elongating stem (ES) and post-elongation stem (PES) internodes of 708 and 773. These ESTs were de novo assembled into 132,153 unique sequences. By combining the de novo assembled ESTs (132,153 sequences) with our previously identified EST sequences (341,984 sequences, unpublished data), and the ESTs available from GenBank (12,371 sequences), we built the first Alfalfa Gene Index (MSGI 1.0). MSGI 1.0 contains 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. We identified a total of 1, 294 simple sequence repeats (SSR) among the sequences in MSGI 1.0. In addition, a total of 10,826 single nucleotide polymorphisms (SNPs) were predicted between the two genotypes. Transcript profiling of stem internodes of genotypes 708 and 773 was conducted by quantifying the number of Illumina EST reads that were mapped to sequences in MSGI 1.0. We identified numerous candidate genes that may play a role in stem development as well as candidate genes that may contribute to the differences in cell wall composition in stems of the two genotypes. Our results demonstrate that RNA-Seq can be successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index (MSGI 1.0) assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a cellulosic feedstock.
2011-04-21 | GSE26757 | GEO
Project description:To explore the molecular regulatory mechanisms of early stem and leaf development, proteomic analysis was performed on leaves and stems of F genotype alfalfa, with thin stems and small leaves, and M genotype alfalfa, with thick stems and large leaves.
2020-11-13 | PXD022535 |
Project description:Alfalfa (Medicago sativa L.) is a forage legume with significant agricultural value worldwide. MicroRNAs (miRNAs) are key components of post-transcriptional gene regulation and essentially control almost all aspect of plant growth and development. Although miRNAs have been reported from alfalfa but their expression profiles in different tissues and novel miRNAs as well as their targets have not been confirmed in this plant species. Therefore, we sequenced small RNAs in whole plantlets, shoots and roots of three different alfalfa genotypes (Altet-4, NECS-141 and NF08ALF06) to identify tissue-specific profiles. After comprehensive analysis using bioinformatics methods, we have identified 100 miRNA families, of which 21 belongs to the highly conserved families whereas the remaining 79 families are conserved between M. truncatula and M. sativa. The profiles of the six highly expressed conserved miRNA families (miR156, 159, 166, 319, 396, 398,) were relatively similar between the plantlets, roots and shoots of three genotypes. Contrastingly, the differenecs were robust between shoots and roots for miR160 and miR408 levels, which were low in roots compared to shoots. The study also has identified 17 novel miRNAs that also differed in their abundanecs between tissues of the alfalfa genotypes. Additionally, we have generated and analyzed the degradome libraries from three alfalfa genotypes that has confirmed 69 genes as targets for 31 miRNA families in alfalfa. The identification of conserved and novel miRNAs as well as their targets in different tissues of three genotypes not only enhanced our understanding of miRNA-mediated gene regulation in alfalfa but could also be useful for practical applications in alfalfa as well as related legume species.
2019-01-15 | GSE119460 | GEO
Project description:With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa. Three lines of Alfalfa (salt-tolerant CW064027, salt-tolerant Bridgeview, salt-sensitive Rangelander) were grown on 3 different concentrations of salt. For each cultivar-salt condition, 3 biological replicates were collected for a total of 27 samples.
2016-07-26 | E-GEOD-84825 | biostudies-arrayexpress
Project description:With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive Western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p < 0.05) were down-regulated in the salt-sensitive population growing under high salinity, while remaining unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population were observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.
2016-07-26 | GSE84825 | GEO
Project description:Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We selected two alfalfa genotypes (252, 1283) that differ in cellulose and Klason lignin concentration in stem cell walls. Analysis of GeneChip expression data files of alfalfa stem internodes of genotypes 252 and 1283 at two growth stages (elongating, post-elongation) revealed 10,887 SFPs in 8,230 probe sets. Validation analysis by PCR-sequencing of a random sample of SFPs indicated a 12% false discovery rate. Functional classification and over-representation analysis showed that both genotypes were highly enriched in SFP-harboring cell wall genes. We mapped 5,833 of the 8,230 SFP-harboring genes onto putative orthologous loci on Medicago truncatula chromosomes. Clustering and over-representation of SFP-harboring genes within the same functional class (e.g. cell wall genes) was observed on some chromosomes. Prior to analysis of expression data for the two alfalfa genotypes, SFP probes were masked to reduce false positives and false negatives. The combination of SFP and gene expression analysis provide a list of candidate cell wall genes that can be used as molecular markers in a breeding program to improve alfalfa as a cellulosic feedstock. The results of this study will also be useful in advancing understanding of genome organization in alfalfa and for comparative genomics research with other legume species. Keywords: Stem development and genotype comparison
2009-05-28 | GSE13602 | GEO
Project description:Abstract: In order to understand the expression patterns of miRNAs in alfalfa under alkali stress, small RNA sequencing was performed on alfalfa roots at different time points under alkali stress, and miRNAs were identified and analyzed.
2023-05-08 | GSE231697 | GEO
Project description:Advances in alfalfa [Medicago sativa (L.) subsp. sativa] breeding, molecular genetics and genomics have been slow because this crop is an allogamous autotetraploid (2n = 4x = 32) with complex polysomic inheritance. Increasing cellulose and decreasing lignin in alfalfa stem cell walls would improve this crop as a cellulosic ethanol feedstock. We selected two alfalfa genotypes (252, 1283) that differ in cellulose and Klason lignin concentration in stem cell walls. Analysis of GeneChip expression data files of alfalfa stem internodes of genotypes 252 and 1283 at two growth stages (elongating, post-elongation) revealed 10,887 SFPs in 8,230 probe sets. Validation analysis by PCR-sequencing of a random sample of SFPs indicated a 12% false discovery rate. Functional classification and over-representation analysis showed that both genotypes were highly enriched in SFP-harboring cell wall genes. We mapped 5,833 of the 8,230 SFP-harboring genes onto putative orthologous loci on Medicago truncatula chromosomes. Clustering and over-representation of SFP-harboring genes within the same functional class (e.g. cell wall genes) was observed on some chromosomes. Prior to analysis of expression data for the two alfalfa genotypes, SFP probes were masked to reduce false positives and false negatives. The combination of SFP and gene expression analysis provide a list of candidate cell wall genes that can be used as molecular markers in a breeding program to improve alfalfa as a cellulosic feedstock. The results of this study will also be useful in advancing understanding of genome organization in alfalfa and for comparative genomics research with other legume species. SUBMITTER_CITATION: Mesfin Tesfaye, S.S. Yang, J.F. Lamb, H.J. Jung, D.A. Samac, J. Gronwald, C.P. Vance and K.A. VandenBosch (2009). Medicago truncatula as a model for dicot cell wall development. BioEnergy Research 2: 59-76 Experiment Overall Design: The alfalfa clonal lines 252 and 1283 were propagated from cuttings and grown in the greenhouse. The greenhouse experiments consisted of three replicates arranged in a randomized complete block design. There were eight plants of each clone, in individual pots, in each replicate. Plant material for analysis was composited within each replicate at harvest. Stem internode tissues were harvested at full bloom. Based on tissue pliability and coloration, the internode in transition from elongation to post-elongation cambial growth was identified. The internodes immediately above (elongating internodes) and below this transition internode (post-elongation internodes) were collected for RNA extraction.
2009-06-08 | E-GEOD-13602 | biostudies-arrayexpress