TY - JOUR
T1 - The STR120 satellite DNA of soybean
T2 - Organization, evolution and chromosomal specificity
AU - Morgante, M.
AU - Jurman, I.
AU - Shi, L.
AU - Zhu, T.
AU - Keim, P.
AU - Rafalski, J. A.
N1 - Funding Information:
We are grateful to Phyllis Biddle for her excellent technical assistance. Financial support from the North Atlantic Treaty Organization (CRG 940005) is gratefully
PY - 1997
Y1 - 1997
N2 - A highly repeated DNA sequence family, STR120, with tandemly arranged repetitive units (monomers) approximately 120 bp, has been identified in soybean [Glycine max (L.) Merr.]. Five related clones showing tandem repeats of a 120-bp-long monomer were isolated from a soybean genomic library. Results of Southern blotting experiments using three of the clones as probes onto genomic DNA digested with different restriction enzymes were in agreement with a tandem arrangement of these sequences in the genome. A total of 12 monomers were sequenced, showing considerable sequence heterogeneity. A consensus sequence of 126 bp was obtained that exhibits an average similarity of 81% to the sequenced units. In three of the clones identified, neighbouring units are significantly more similar to each other than to units from different clones; in the remaining two clones, however, similarity between the two units observed is low (70%), while the overall similarity between the two clones is high (95%). This indicates that in these cases the repetitive unit may be the dimer rather than the monomer. Based on the presence of direct repeats within each monomer, we suggest that the 120-bp monomer may itself have evolved by duplication of an ancestral 60-bp unit. The STR120 family distribution is limited to annual soybeans and is not found, at least at high-copy number, in related perennial soybeans or other members of the tribe Phaseolae. Fluorescence in situ hybridization (FISH) to metaphase chromosomes using four of the clones as probes shows that the number of chromosomal locations differs depending on the stringency conditions and goes from two to eight when the stringency is progressively lowered. The estimated copy number for one of the clones is from 5000 to 10,000, but this may just represent a lower boundary for the whole family in consideration of the high sequence divergence observed within the family. FISH and sequence analysis therefore indicate that different subfamilies as well as higher-order repeat units are present in the STR120 family, very much like those in primate alpha satellite DNA, and that some of the subfamilies seem to exhibit divergence on a chromosomal basis.
AB - A highly repeated DNA sequence family, STR120, with tandemly arranged repetitive units (monomers) approximately 120 bp, has been identified in soybean [Glycine max (L.) Merr.]. Five related clones showing tandem repeats of a 120-bp-long monomer were isolated from a soybean genomic library. Results of Southern blotting experiments using three of the clones as probes onto genomic DNA digested with different restriction enzymes were in agreement with a tandem arrangement of these sequences in the genome. A total of 12 monomers were sequenced, showing considerable sequence heterogeneity. A consensus sequence of 126 bp was obtained that exhibits an average similarity of 81% to the sequenced units. In three of the clones identified, neighbouring units are significantly more similar to each other than to units from different clones; in the remaining two clones, however, similarity between the two units observed is low (70%), while the overall similarity between the two clones is high (95%). This indicates that in these cases the repetitive unit may be the dimer rather than the monomer. Based on the presence of direct repeats within each monomer, we suggest that the 120-bp monomer may itself have evolved by duplication of an ancestral 60-bp unit. The STR120 family distribution is limited to annual soybeans and is not found, at least at high-copy number, in related perennial soybeans or other members of the tribe Phaseolae. Fluorescence in situ hybridization (FISH) to metaphase chromosomes using four of the clones as probes shows that the number of chromosomal locations differs depending on the stringency conditions and goes from two to eight when the stringency is progressively lowered. The estimated copy number for one of the clones is from 5000 to 10,000, but this may just represent a lower boundary for the whole family in consideration of the high sequence divergence observed within the family. FISH and sequence analysis therefore indicate that different subfamilies as well as higher-order repeat units are present in the STR120 family, very much like those in primate alpha satellite DNA, and that some of the subfamilies seem to exhibit divergence on a chromosomal basis.
KW - Duplication
KW - Fluorescence in situ hybridization
KW - Repetitive DNA
KW - Sequence divergence
UR - http://www.scopus.com/inward/record.url?scp=0030733459&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0030733459&partnerID=8YFLogxK
U2 - 10.1023/A:1018492208247
DO - 10.1023/A:1018492208247
M3 - Article
C2 - 9364938
AN - SCOPUS:0030733459
SN - 0967-3849
VL - 5
SP - 363
EP - 373
JO - Chromosome Research
JF - Chromosome Research
IS - 6
ER -