Background: Gymnosperms 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. Results: Here, 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. Conclusions: We 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.

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 transfer/loss 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 variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.

Tribe Theeae, which includes some economically important and widely grown plants, such as beverage tea and a number of woody ornamentals, is the largest member of the Theaceae family. Using five genomic regions (chloroplast: atpI-H, matK, psbA5'R-ALS-11F, rbcL; nuclear: LEAFY) and 30 species representing four of the five genera in this tribe (Apterosperma, Camellia, Polyspora, and Pyrenaria s.l.), we investigated the phylogeny of Theeae and assessed the delimitation of genera in the tribe. Our results showed that Polyspora was monophyletic and the sister of the three other genera of Theeae investigated, Camellia was paraphyletic and Pyrenaria was polyphyletic. The inconsistent phylogenetic placement of some species of Theeae between the nuclear and chloroplast trees suggested widespread hybridization between Camellia and Pyrenaria, Polyspora and Parapyrenaria. These results indicate that hybridization, rather than morphological homoplasy, has confused the current classification of Theeae. In addition, the phylogenetic placement and possible allies of Laplacea are also discussed.

Background Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism. Results Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa. Conclusions We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.

TCP proteins are plant-specific transcription factors, which are involved in a broad range of physiological processes of plant growth and development. However, the origin and evolutionary history of this gene family is not fully resolved. Here, we present a genome-wide survey of TCP genes in 59 species (including 42 genomes and 17 transcriptomes) covering all main lineages of green plants, and reconstruct the evolutionary history of this gene family. Our results suggested that the origin of TCP genes predated the emergence of land plants, possibly in the common ancestor of Phragmoplastophyta. The TCP gene family gradually experienced a continuous expansion and grew from a few members in algae, moss and lycophytes to dozens, and sometimes over 50 members in angiosperms. Phylogenetic analysis indicated that at least four subclades (Class I and three subclades of Class II) have been occurred in the ancestor of spermatophyte (seed plant). Both dispersed duplication and segmental duplication or whole-genome duplication (WGD) contributed significantly to the expansion of the TCP gene family over the course of evolution. Our findings provide a comprehensive evolutionary analysis of the TCP gene family and highlight the importance of gene duplications in the evolution of this plant-specific transcription factors.

The genus Broussonetia (Moraceae) is comprised of three non-hybrid recognized species that all produce high quality fiber essential in the development of papermaking and barkcloth-making technology. In addition, these species also have medicinal value in several countries. Despite their important economical, medicinal, and ecological values, the complete mitogenome of Broussonetia has not been reported and investigated, which would greatly facilitate molecular phylogenetics, species identification and understanding evolutionary processes. Here, we assembled the first-reported three complete Broussonetia (B. papyrifera, B. kaempferi, and B. monoica) mitochondrial genomes (mitogenome) based on a hybrid strategy using Illumina and Oxford Nanopore Technology sequencing data, and performed comprehensive comparisons in terms of their structure, gene content, synteny, intercellular gene transfer, phylogeny, and RNA editing. Our results showed their huge heterogeneities among the three species. Interestingly, the mitogenomes of B. monoica and B. papyrifera consisted of a single circular structure, whereas the B. kaempferi mitogenome was unique and consisted of a double circular structure. Gene content was consistent except for a few transfer RNA (tRNA) genes. The Broussonetia spp. mitogenomes had high sequence conservation but B. monoica with B. kaempferi contained more synteny blocks and were more related, a finding that was well-supported in organellar phylogeny. Fragments that had been transferred between mitogenomes were detected at plastome hotspots that had integrated under potential mediation of tRNA genes. In addition, RNA editing sites showed great differences in abundance, type, location and efficiency among species and tissues. The availability of these complete gap-free mitogenomes of Broussonetia spp. will provide a valuable genetic resource for evolutionary research and understanding the communications between the two organelle genomes.

There is a paradox in the plant mitochondrial genome, that is, the genic region evolves slowly while the intergenic region evolves rapidly. Thus, the intergenic regions of the plant mitochondrial genome are difficult to align across different species, even in closely related species. Here, to character the mechanism of this paradox, we identified interspecific variations in the Ginkgo biloba, Oryza sativa, and Arabidopsis thaliana mitochondrial and plastid genome at a genome-wide level. The substitution rate of synonymous sites in genic regions was similar to the substitution rate of intergenic regions, while the substitution rate of nonsynonymous sites in genic regions was lower than that in intergenic regions, suggesting the mutation inputs were the same among different categories within the organelle genome, but the selection pressure varied. The substitution rate of single-copy regions was higher than that of IR (inverted repeats) in the plastid genome at an intraspecific level. The substitution rate of single-copy regions was higher than that of repeats in the G. biloba and A. thaliana mitochondrial genomes, but lower in that of O. sativa. This difference may be related to the length and distribution of repeats. Copy number variations that existed in the G. biloba and O. sativa mitochondrial genomes were confirmed. This study reveals the intraspecific variation pattern of organelle genomes at a genome-wide level, and that copy number variations were common in plant mitochondrial genomes.

Corydalis DC., the largest genus of Papaveraceae, was recognized as one of the most taxonomically challenging plant taxa. Due to the lack of genetic information used in previous studies, species discrimination and taxonomic assignment in Corydalis have not been fully solved. Here, the complete chloroplast genomes were reported for Corydalis edulis Maxim. and Corydalis shensiana Liden, with their genome sizes being 154,395 and 155,938 bp, respectively. Both of the chloroplast genomes comprise two inverted repeat (IR) regions, separated by a large single-copy (LSC) region and a small single-copy (SSC) region, and encode 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, 37 transfer RNA genes. Our study will provide novel insight into the molecular phylogeny and classification of Corydalis.