ArticleBMC genomics2015
The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 95 citations in OpenAlex.
- Genome-wide characterization and expression analysis of the B3 superfamily in response to abiotic stresses in alfalfa (Medicago sativa L.).BMC plant biology · 2026Article
- Characterization of the BPC genes in alfalfa and functional verification of MsBPC10 in salt tolerance.BMC plant biology · 2026Article
- BacA(SbmA) importer of legume symbiotic NCR peptides: Protein architecture, function, and evolutionary implications.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genome-wide identification and characterization ofFrontiers in plant science · 2026Article
- Genome-wide identification and analysis of the abiotic stress responsiveness of the heat shock protein 90 gene family in Medicago sativa L.BMC plant biology · 2025Article
- Genome-wide identification and expression pattern analysis of the CPP transcription factor family in Medicago sativa L.BMC plant biology · 2025Article
- Genome-wide characterization of NHX gene family in Medicago sativa under abiotic stress.BMC plant biology · 2025Article
- Genome-wide identification and expression analysis of the GARP superfamily in response to abiotic stresses in alfalfa (Medicago sativa L.).BMC plant biology · 2025Article
- Genome-wide identification and expression analysis of the class III peroxidase gene (PRXIII) family in Medicago sativa L. and its function in the abiotic stress response.BMC plant biology · 2025Article
- Potential Effect of Root Exudates from Ten Crops on Promoting Stress Tolerance in Alfalfa (Life (Basel, Switzerland) · 2025Article
- Genome-wide identification and comprehensive analysis of theFrontiers in plant science · 2025Article
- Genome-Wide Identification, Phylogenetic, and Expression Analysis of Jasmonate ZIM-Domain Gene Family inInternational journal of molecular sciences · 2024Article
- Genome-wide identification and analysis of abiotic stress responsiveness of the mitogen-activated protein kinase gene family in Medicago sativa L.BMC plant biology · 2024Article
- Genome-wide identification of SHMT family genes in alfalfa (Medicago sativa) and its functional analyses under various abiotic stresses.BMC genomics · 2024Article
- A genome-wide association study reveals novel loci and candidate genes associated with plant height variation in Medicago sativa.BMC plant biology · 2024Article
- In silico analysis identified bZIP transcription factors genes responsive to abiotic stress in Alfalfa (Medicago sativa L.).BMC genomics · 2024Article
- Genome-wide identification of B-box zinc finger (BBX) gene family in Medicago sativa and their roles in abiotic stress responses.BMC genomics · 2024Article
- MODMS: a multi-omics database for facilitating biological studies on alfalfa (Horticulture research · 2024Article
- Characterization of the Heat Shock Transcription Factor Family inInternational journal of molecular sciences · 2023Article
- Genome-Wide Identification and Phylogenetic and Expression Analyses of theInternational journal of molecular sciences · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement.
resultsA de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.
conclusionsThe Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/ , a publicly available genomic resource for alfalfa improvement and legume research.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.