Data for: Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome

Background: Mitochondrial gene transfer/loss is common in land plants, and
therefore the fate of missing mitochondrial genes has attracted more and
more attention. The gene content of gymnosperm mitochondria varies
greatly, supplying a system for studying the evolutionary fate of missing
mitochondrial genes. Results: Here we studied the tempo and pattern of
mitochondrial gene loss/transfer in gymnosperms represented by all 13
families, using high-throughput sequencing of both DNA and cDNA. All 41
mitochondrial protein-coding genes were found in cycads, Ginkgo and
Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II
and Gnetales. In Conifer II, gene transfer from mitochondria to the
nucleus followed by loss of the mitochondrial copy was common, but
complete loss of a gene in both mitochondrial and nuclear genomes was
rare. In contrast, both gene transfer and loss were commonly found in
Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial
genes were transferred to the nuclear genome, and these gene transfer
events occurred, respectively, in ancestors of the two lineages. A
two-step transfer mechanism (retroprocessing and subsequent DNA-mediated
gene transfer) may be responsible for mitochondrial gene transfer in
Conifer II and Gnetales. Moreover, the mitochondrial gene content
variation is correlated with gene length, GC content, hydrophobicity, and
nucleotide substitution rates in land plants. Conclusions: This study
reveals a complete evolutionary scenario for mitochondrial genes of
gymnosperms and the factors responsible for mitochondrial gene content
variation in land plants.