Abstract
BackgroundGymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms.ResultsHere, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species.ConclusionsWe have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.
Highlights
Gymnosperms represent five of the six lineages of seed plants
We identified tRNA genes, introns, and open reading frames (ORFs) in all five mitogenomes (Cycas taitungensis, Ginkgo biloba, Pinus taeda, Taxus cuspidata, and Welwitschia mirabilis). tRNA genes were identified by tRNAscan-SE 2.0 [35], and group I and II introns were detected by the RNAweasel tool [25]
Multiple mitochondrial RNA editing sites have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms [46]
Summary
Gymnosperms represent five of the six lineages of seed plants. most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. Based on the recent phylogenomic study of Ran et al [8], gymnosperms represent five of the six main lineages of seed plants, namely, cycads, ginkgo, gnetophytes, Pinaceae and Conifer II (non-Pinaceae conifers or Cupressophyta) [9, 10]. These lineages diverged before the Jurassic and have diversified dramatically in morphological characters and molecular evolutionary rates [8, 11]. Knowledge of mitogenomic features in Conifer II is essential for a comprehensive understanding of the evolution and diversification of gymnosperm mitogenomes
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