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Frequent pseudogenization and loss of the plastid‐encoded sulfate‐transport gene cys A throughout the evolution of liverworts
Author(s) -
Wickett Norman J.,
Forrest Laura L.,
Budke Jessica M.,
Shaw Blanka,
Goffinet Bernard
Publication year - 2011
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1100010
Subject(s) - biology , nonsynonymous substitution , plastid , pseudogene , genetics , gene , phylogenetic tree , genome , negative selection , synonymous substitution , phylogenetics , chloroplast , codon usage bias
• Premise of the study: The presence or absence of a functional copy of a plastid gene may reflect relaxed selection, and may be phylogenetically significant, reflecting shared ancestry. In some liverworts, the plastid gene cys A is a pseudogene (inferred to be nonfunctional). We surveyed 63 liverworts from all major clades to determine whether the loss of cys A is phylogenetically significant, whether intact copies of cys A are under selective constraints, and whether rates of nucleotide substitution differ in other plastid genes from taxa with and without a functional copy of cys A. • Methods: Primers annealing to flanking and internal regions were used to amplify and sequence cys A from 61 liverworts. Two additional cys A sequences were downloaded from NCBI. The ancestral states of cys A were reconstructed on a phylogenetic hypothesis inferred from seven markers. Rates of nucleotide substitution were estimated for three plastid loci to reflect the intrinsic mutation rate in the plastid genome. The ratio of nonsynonymous to synonymous substitutions was estimated for intact copies of cys A to infer selective constraints. • Key results: Throughout liverworts, cys A has been lost up to 29 times, yet intact copies of cys A are evolving under selective constraints. Gene loss is more frequent in groups with an increased substitution rate in the plastid genome. • Conclusions: The number of inferred losses of cys A in liverworts exceeds any other reported plastid gene. Despite frequent losses, cys A is evolving under purifying selection in liverworts that retain the gene. It appears that cys A is lost more frequently in lineages characterized by a higher rate of nucleotide substitutions in the plastid.