Zhiqiang Wu

Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. The draft genome of the Norway spruce (P. abies) is presented; this is the first gymnosperm genome to be sequenced and reveals a large genome size (20 Gb) resulting from the accumulation of transposable elements, and comparative sequencing of five other gymnosperm genomes provides insights into conifer genome evolution. The first draft gymnosperm genome, that of a Norway spruce (Picea abies), is published this week by the Spruce Genome Project consortium. The genome is from a tree originally collected in 1959 in eastern Jämtland, central Sweden. At 20 gigabases, the genome is more than a hundred times larger than that of the model plant species Arabidopsis, but the two contain a similar number of genes. The large genome size is the result of an accumulation of transposable elements. Comparative sequencing of five further gymnosperm genomes suggests that transposable element diversity is shared among extant conifers. The sequence data are available for public access from the ConGenIE website ( http://congenie.org/ ).

Abstract Since the endosymbiont origin from α‐Proteobacteria, mitochondrial genomes have undergone extremely divergent evolutionary trajectories among eukaryotic lineages. Compared with the relatively compact and conserved animal mitochondrial genomes, plant mitochondrial genomes have many unique features, especially their large and complex genomic arrangements. The sizes of fully sequenced plant mitochondrial genomes span over a 100‐fold range from 66 kb in Viscum scurruloideum to 11 000 kb in Silene conica . In addition to the typical circular structure, some species of plants also possess linear, and even multichromosomal, architectures. In contrast with the thousands of fully sequenced animal mitochondrial genomes and plant plastid genomes, only around 200 fully sequenced land plant mitochondrial genomes have been published, with many being only draft assemblies. In this review, we summarize some of the known novel characteristics found in plant mitochondrial genomes, with special emphasis on multichromosomal structures described in recent publications. Finally, we discuss the future prospects for studying the inheritance patterns of multichromosomal plant mitochondria and examining architectural variation at different levels of taxonomic organization—including at the population level.

Abstract The tuatara ( Sphenodon punctatus )—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana 1,2 —is an iconic species that is endemic to New Zealand 2,3 . A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes 2,4 . Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.