Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus.

@article{Clough2004FeaturesOA,
  title={Features of a 103-kb gene-rich region in soybean include an inverted perfect repeat cluster of CHS genes comprising the I locus.},
  author={Steven John Clough and Jigyasa H. Tuteja and Min Li and Laura Fredrick Marek and Randy C. Shoemaker and Lila O. Vodkin},
  journal={Genome},
  year={2004},
  volume={47 5},
  pages={
          819-31
        }
}
The I locus in soybean (Glycine max) corresponds to a region of chalcone synthase (CHS) gene duplications affecting seed pigmentation. We sequenced and annotated BAC clone 104J7, which harbors a dominant i(i) allele from Glycine max 'Williams 82', to gain insight into the genetic structure of this multigenic region in addition to examining its flanking regions. The 103-kb BAC encompasses a gene-rich region with 11 putatively expressed genes. In addition to six copies of CHS, these genes include… 

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References

SHOWING 1-10 OF 61 REFERENCES
Tissue-Specific Gene Silencing Mediated by a Naturally Occurring Chalcone Synthase Gene Cluster in Glycine max
TLDR
Increase in pigmentation in the black seed coats was associated with release of the silencing effect specifically on CHS7/CHS8, which occurred at all stages of seed coat development.
Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G.
TLDR
The results extend previous observations of large-scale duplication and selective gene loss in Arabidopsis, suggesting that networks of conserved synteny betweenArabidopsis and other angiosperm families can stretch over long physical distances.
Duplications That Suppress and Deletions That Restore Expression from a Chalcone Synthase Multigene Family.
TLDR
It is demonstrated that the / locus is a region of chalcone synthase (CHS) gene duplications that allows higher levels of CHS mRNAs and restore pigmentation to the seed coat and that the spontaneous deletions erase the gene-silencing phenomena.
Organization, expression and evolution of a disease resistance gene cluster in soybean.
TLDR
Analysis of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process, and identifies 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes.
Structural analysis of a Lotus japonicus genome. I. Sequence features and mapping of fifty-six TAC clones which cover the 5.4 mb regions of the genome.
A total of 56 TAC clones with an average insert size of 100 kb were isolated from a TAC library of the Lotus japonicus genome based on the expressed sequences tags (ESTs), cDNA and gene information,
Genome duplication in soybean (Glycine subgenus soja).
TLDR
Quantitative trait loci for seed protein and oil showed correspondence across homoeologous regions, suggesting that the genes or gene families contributing to seed composition have retained similar functions throughout the evolution of the chromosomes.
Analysis of the duplicated CHS1 gene related to the suppression of the seed coat pigmentation in yellow soybeans
TLDR
The results showed that the duplicated CHS1 contained intact regulatory and coding regions and was designated as ICHS1, which was closely linked to the truncated CHS3, and sequence comparison showed that this cluster probably arose from the CHS 1–CHS3 cluster by a 1.8-kb deletion event.
Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome.
Sixty-five TAC (transformation-competent artificial chromosomes) clones were selected from a genomic library of Lotus japonicus accession MG-20 based on the sequence information of expressed
The chalcone synthase multigene family of Petunia hybrida (V30): sequence homology, chromosomal localization and evolutionary aspects
TLDR
Analysis of the Petunia species that contributed to the hybrid nature of P. hybrida shows that none of the CHS gene clusters is specific for either one of the parents and therefore did not arise as a consequence of the hybridization, inferring that theCHS subfamilies arose from very recent gene duplications.
Differential regulation of soybean chalcone synthase genes in plant defence, symbiosis and upon environmental stimuli
TLDR
The authors' results suggest a co-operative induction of CHS genes by wounding and clicitor treatment of cotyledons of soybean seedlings, and possible involvement of different members of the CHS gene family in response to elicitor versus UV treatment.
...
1
2
3
4
5
...