Phylogenetic relationships of the chloroplast genomes in the genus Glycine inferred from four intergenic spacer sequences

Abstract

The nucleotide sequences of four intergenic spacer regions of chloroplast DNA, atpB-rbcL, trnS-trnG, rps11-rpl36, and rps3-rpl16, were analyzed in the genus Glycine. Phylogenetic analysis based on the sequence data using Neonotonia wightii as the outgroup generated trees supporting the classification of two subgenera, Soja and Glycine, and three plastome groups in the subgenus Glycine. The results were consistent with the presence of diversified chloroplast genomes within tetraploid plants of G. tabacina and G. tomentella, as well as with a close relationship between G. tomentella and G. dolichocarpa that had been suggested based on morphological analyses. Little sequence variation was found in the subgenus Soja, suggesting that G. soja rapidly expanded its distribution in East Asia. The analysis also showed that the differentiation into three plastome groups in the subgenus Glycine occurred in the early stages of its evolution, after the two subgenera diverged

A Preliminary Comparative Evaluation of Genetic Diversity between Chinese and Japanese Wild Soybean (Glycine soja) Germplasm Pools using SSR markers

“…Japan also is one of the wild soybean provenances but it is by sea from the other land areas of wild soybean distribution. Sakai et al (2003) analysed four intergenic spacer regions of chloroplast DNA in the genus Glycine and deemed that G. soja spread rapidly in east Asia after the origination of G. soja. However, the present results strongly indicate a tendency that Japanese and Chinese wild soybean pools have greater genetic difference, as shown by the genetic distances in Table 6.…”

Genetic spatial clustering: significant implications for conservation of wild soybean (Glycine soja: Fabaceae)

“…However, intrinsic differences in genetic diversity may also explain the different results for wild soybean populations in China and Japan, given that ISSR is a neutral marker, and genetic differentiation revealed among the populations was the reflection of isolation-by-distance (Bornet et al, 2002). In fact, some studies already demonstrated a greater genetic variability in wild soybean collected from Japan than from China (Sakai et al, 2003).…”

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

“…92 AMERICAN JOURNAL OF BOTANY gaceae clade, and Xu et al (2000) showed the trnS-trnG spacer to be among the most informative of nine noncoding cpDNA regions within two closely related subgenera of Glycine. In another study within Glycine, Sakai et al (2003) showed the trnS-trnG spacer to contain many more PICs than atpB-rbcL, rpS11-rpL36, and rpS3-rpL16. The trnS-trnG spacer was reported to show intraspecific variation in Moringa (Moringaceae) by Olson (2002b) and Corythophora (Lecythidaceae) by Hamilton (1999a, b).…”

“…It has been clearly shown that the phylogenetic utility of different noncoding cpDNA regions within a given taxonomic group can vary tremendously (Sang et al, 1997;Small et al, 1998;Xu et al, 2000;Hartmann et al, 2002;Mast and Givnish, 2002;Cronn et al, 2002;Hamilton et al, 2003;Perret et al, 2003;Sakai et al, 2003), but choosing an appropriate cpDNA region for phylogenetic investigation is often difficult because of the paucity of information about the relative tempo of evolution among different noncoding cpDNA regions. Gielly and Taberlet (1994, p. 774) wrote: ''it is not easy, for many reasons, to establish a rule for the choice of a particular region of the chloroplast genome for resolving phylogenies.''…”

“…Gielly and Taberlet (1994, p. 774) wrote: ''it is not easy, for many reasons, to establish a rule for the choice of a particular region of the chloroplast genome for resolving phylogenies.'' While many authors have compared relative rates of evolution among a few noncoding regions (Sang et al, 1997;Small et al, 1998;Wang et al, 1999;Kusumi et al, 2000;Xu et al, 2000;Soltis et al, 2001;Cronn et al, 2002;Mast and Givnish, 2002;Hamilton et al, 2003;Perret et al, 2003;Sakai et al, 2003;Yamane et al, 2003), these studies are all of a relatively narrow phylogenetic context and there is no consensus as to variability in evolutionary rates among noncoding cpDNA regions across a broad phylogenetic range. To our knowledge, the only work that has attempted to compare levels of variation among several different noncoding cpDNA regions across a wide range of lineages is Aoki et al (2003).…”