Small subunit ribosomal RNA sequences from Ginkgo biloba and phylogenetic inferences from seed plant small subunit ribosomal RNA data

Ginkgo biloba is a taxonomically isolated seed plant frequently placed in an evolutionary grade group referred to as gymnosperms. Precise phylogenetic relationships between Ginkgo and other gymnosperm groups remain uncertain. Small subunit ribosomal DNA sequences were isolated from a Ginkgo genomic library. One group of clones represents the small subunit rRNA genes from the major ribosomal repeat of Ginkgo and are present in approximately 16,000 copies in the diploid Ginkgo genome. A representative, Gbr-1000, from this group was subcloned and sequenced. A representative, Gbr-6700, from a second group of clones was also sequenced and contains a ss rRNA-like sequence that is interrupted by a 1.1 kb insert 700 bp into the ss rRNA-like region. These ss rRNA-like sequences are present in approximately 3,400 copies in the Ginkgo genome. The Gbr-1000 sequence was compared with homologous sequences from other green plant taxa. Phylogenetic relationships of these taxa were inferred using a cladistic parsimony analysis of the combined sequence data. A single most parsimonious tree was found which supports a monophyletic grouping of Ginkgo and the cycad Zamia pumila. The Gbr-6700 sequence was compared with that of Gbr-1000. The homologous regions of the two Ginkgo sequences are 86% similar compared with 92%-97% sequence similarities observed between ss rRNA sequences of available seed plant taxa. The Gbr-6700 sequence represents a ss rRNA pseudogene which is present in multiple copies in the Ginkgo genome. These sequences appear to be undergoing concerted evolution within the group, similar to that observed for eukaryotic rRNA gene families.