Intron sequences provide a tool for high-resolution phylogenetic analysis of volvocine algae

Abstract

Three nuclear spliceosomal introns in conserved locations were amplified and sequenced from 28 strains representing 14 species and 4 genera of volvocalean green algae. Data derived from the three different introns yielded congruent results in nearly all cases. In pairwise comparisons, a spectrum of taxon-specific sequence differences ranging from complete identity to no significant similarity was observed, with the most distantly related organisms lacking any conserved elements apart from exon-intron boundaries and a pyrimidine-rich stretch near the 3' splice site. A metric (SI50), providing a measure of the degree of similarity of any pair of intron sequences, was defined and used to calculate phylogenetic distances between organisms whose introns displayed statistically significant similarities. The rate of sequences divergence in the introns was great enough to provide useful information about relationships among different geographical isolates of a single species, but in most cases was too great to provide reliable guides to relationships above the species level. A substitution rate of approximately 3 x 10(-8) per intron position per year was estimated, which is about 150-fold higher than in nuclear genes encoding rRNA and about 10-fold higher than the synonymous substitution rate in protein-coding regions. Thus, these homologous introns not only provide useful information about intraspecific phylogenetic relationships, but also illustrate the concept that different parts of a gene may be subject to extremely different intensities of selection. The intron data generated here (1) reliably resolve for the first time the relationships among the five most extensively studied strains of Volvox, (2) reveal that two other Volvox species may be more closely related than had previously been suspected, (3) confirm prior evidence that particular isolates of Eudorina elegans and Pleodorina illinoisensis appear to be sibling taxa, and (4) contribute to the resolution of several hitherto unsettled issues in Chlamydomonas taxonomy.

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii

“…Nucleotide diversity in the field strains (p = 0.028) is comparable to previous reports based on nuclear gene sequences (p intron = .027 [Liss et al, 1997;Sung et al, 2012], p silent = 0.032, p intron = 0.033 [Smith and Lee, 2008]), although higher than estimates from other studies (Jang and Ehrenreich, 2012) (Table 5). Using this diversity estimate and two independent measures of the spontaneous mutation rate, m, for Chlamydomonas (Ness et al, 2012;Sung et al, 2012), we estimate the effective population size, N e = p/2m, to be on the order of 10 8 .…”

Rapid evolution of sex-related genes in Chlamydomonas

“…The one detected interspecies mid homolog is found in C. incerta, a species shown here and by others (5,6), to be the closest C. reinhardtii relative in culture although they fail to mate. The mid genes of these two species prove to carry nonsynonymous codon differences at 35͞148 positions (24%) and synonymous codon differences at 32͞148 positions (22%).…”

“…The primers used were yptC1 upstream and yptC1 downstream (16). The obtained PCR product was purified and sequenced directly by cycle sequencing (6).…”

Evolutionary Rates and Expression Level in Chlamydomonas

“…incerta SAG 7.73 is the closest known noninterfertile relative of C. reinhardtii (Schlö sser 1976; Coleman and Mai 1997;Liss et al 1997;Prö schold et al 2001), with the possible exception of Chlamydomonas sp. (CCAP 11/132) (Prö schold et al 2005).…”

“…(CCAP 11/132) (Prö schold et al 2005). Studies on the level of sequence divergence between C. incerta and C. reinhardtii are limited to three spliceosomal introns (Liss et al 1997), two intergenic spacers (Coleman and Mai 1997), and a few proteincoding genes . Clearly, an expanded analysis of orthologous gene sequences from these taxa is needed to gain a better view of the extent and causes of the variation in evolutionary divergence among genes in Chlamydomonas.…”