ArticleBMC genomics2007
Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 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
82 citing papers in PubMed.
- Calcium signaling in soybean-virus interactions: emerging roles of calcium sensors in antiviral and environmental stress responses.Frontiers in plant science · 2026Review
- Genome-wide identification, expression and evolutionary analysis of the CLC gene family in Vigna radiata L. reveals its roles in salt resistance.BMC genomics · 2025Article
- Evolutionary Conservation and Regulatory Diversification ofInternational journal of molecular sciences · 2025Article
- Article
- Genome-wide identification ofPeerJ · 2024Article
- Comparative Analysis of Circadian Transcriptomes Reveals Circadian Characteristics betweenPlants (Basel, Switzerland) · 2023Article
- Haplotype Analysis of GmSGF14 Gene Family Reveals Its Roles in Photoperiodic Flowering and Regional Adaptation of Soybean.International journal of molecular sciences · 2023Article
- Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses.BMC plant biology · 2023Article
- Genome-Wide Identification and Characterization ofInternational journal of molecular sciences · 2023Article
- Genome-wide identification and expression analysis of diacylglycerol acyltransferase genes in soybean (PeerJ · 2023Article
- Characterization ofFrontiers in genetics · 2023Article
- Risk assessment of a new bioinformatics evaluation of the insertion sites of genetically modified soybean event 40-3-2.EFSA journal. European Food Safety Authority · 2022Article
- Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (International journal of molecular sciences · 2022Article
- Comprehensive genome wide identification and expression analysis ofSaudi journal of biological sciences · 2021Article
- The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis.BMC genomics · 2021Article
- Article
- Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family inFrontiers in genetics · 2021Article
- Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers.Journal of genetics · 2021Article
- Genomic-Wide Analysis of the PLC Family and Detection of GmPI-PLC7 Responses to Drought and Salt Stresses in Soybean.Frontiers in plant science · 2021Article
- Double mutation of two homologous genes YL1 and YL2 results in a leaf yellowing phenotype in soybean [Glycine max (L.) Merr].Plant molecular biology · 2020Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSoybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly.
resultsSeventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences.
conclusionThis analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.
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.