The nuclear ribosomal DNA intergenic spacers of wild and cultivated soybean have low variation and cryptic subrepeats

The intergenic ribosomal DNA spacers (IGSs) from cultivated soybean (Glycine max) and wild soybean (Glycine soja) were sequenced and compared with six other legumes. These IGS sequences were 1821 bp in length in G. soja and G. max cultivars Arksoy, Ransom, and Tokyo, and 1823 bp long in the G. max cultivar Columbus. These represent the smallest published plant IGS sequences to data. Two clones from each of the above five cultivars were sequenced and only 22 sites (1.2%) were polymorphic, thereby supporting previous work that showed low genetic variation in cultivated soybean. The amount of variation observed between different clones derived from the same individual was equal to the amount seen between different cultivars. The soybean IGS sequence was aligned with six other published legume sequences and two homologous regions were identified. The first spans positions 706-1017 in the soybean IGS sequence and ends at a putative promoter site that appears conserved among all legumes. The second is located within the 5' external transcribed spacer, spans positions 1251-1823 in soybean, and includes sequences first identified as subrepeats IV-1 and IV-2 in Vicia angustifolia. Sequences homologous to these two subrepeats were identified among all legume species examined and are here designated "cryptic subrepeats" (CS-1, CS-2) given the range in similarity value (79-96% for CS-1 and 60-95% for CS-2). Comparisons of CS-1 and CS-2 sequences within individual species show that divergence (substitutional mutations, insertions, and deletions) is sufficiently high to obscure recognition of the repeat nature of these sequences by routine dot plot analytical methods. The lack of subrepeats in the 5' half of the soybean IGSs raises questions regarding the role they play in transcription termination or enhancement.