The plastid and mitochondrial genomes of Eucalyptus grandis

Abstract Background Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes. Results In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813 bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis. Conclusions The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species

A systems genetics analysis in Eucalyptus reveals coordination of metabolic pathways associated with xylan modification in wood‐forming tissues

Acetyl‐ and methylglucuronic acid decorations of xylan, the dominant hemicellulose in secondary cell walls (SCWs) of woody dicots, affect its interaction with cellulose and lignin to determine SCW structure and extractability. Genes and pathways involved in these modifications may be targets for genetic engineering; however, little is known about the regulation of xylan modifications in woody plants. To address this, we assessed genetic and gene expression variation associated with xylan modification in developing xylem of Eucalyptus grandis × Eucalyptus urophylla interspecific hybrids. Expression quantitative trait locus (eQTL) mapping identified potential regulatory polymorphisms affecting gene expression modules associated with xylan modification. We identified 14 putative xylan modification genes that are members of five expression modules sharing seven trans‐eQTL hotspots. The xylan modification genes are prevalent in two expression modules. The first comprises nucleotide sugar interconversion pathways supplying the essential precursors for cellulose and xylan biosynthesis. The second contains genes responsible for phenylalanine biosynthesis and S‐adenosylmethionine biosynthesis required for glucuronic acid and monolignol methylation. Co‐expression and co‐regulation analyses also identified four metabolic sources of acetyl coenxyme A that appear to be transcriptionally coordinated with xylan modification. Our systems genetics analysis may provide new avenues for metabolic engineering to alter wood SCW biology for enhanced biomass processability.Supplementary Material: Fig. S1 Phylogram representing a maximum likelihood analysis of RWA proteins in Arabidopsis, Eucalyptus and Populus coupled with relative and absolute percentile expression in xylem and leaf, and domain structure. Fig. S2 Phylogram representing a maximum likelihood analysis of GUX proteins in Arabidopsis, Eucalyptus and Populus coupled with relative and absolute percentile expression in xylem and leaf, and domain structure. Fig. S3 Phylogram representing a maximum likelihood analysis of DUF579/GXM proteins in Arabidopsis, Eucalyptus and Populus coupled with relative and absolute percentile expression in xylem and leaf, and domain structure. Fig. S4 Phylogram representing a maximum likelihood analysis of DUF231/TBL proteins from clade IV in Arabidopsis, Eucalyptus and Populus coupled with relative and absolute percentile expression in xylem and leaf, and domain structure. Fig. S5 Phylogram representing a maximum likelihood analysis of the full complement of DUF231/TBL proteins in Arabidopsis, Eucalyptus and Populus coupled with relative and absolute percentile expression in xylem and leaf, and domain structure. Fig. S6 F‐score threshold determined from the number of genes that each query gene included in the network by using a joint likelihood curve. Fig. S7 Co‐expression and clustering of 1136 genes obtained for genes which passed set criteria divided into five expression modules. Fig. S8 Seventy percent of genes co‐expressed with xylan modification were found to have at least one trans‐eQTL affecting its expression. Fig. S9 Identification of the seven highly enriched trans‐eQTL hotspot loci. Fig. S10 Principal component analysis of the five module eigengenes. Fig. S11 Model of genetic regulation that shapes the expression modules. Fig. S12 Numbers of genes affected by each of the seven hotspot loci and their expression module membership. Fig. S13 Nucleotide sugar interconversion is highly represented in EM5 and regulated primarily by HS_10.3 and HS_10.4. Fig. S14 Complete annotation of Fig. 3 containing genes which were not present in EMs or affected by hotspot loci. Fig. S15 Complete annotation of Fig. 5 containing genes which were not present in EMs or affected by hotspot loci. Methods S1 Network based co‐expression analysis and community detection clustering. Methods S2 Global eQTL mapping and hotspot locus detection. Notes S1 Protein sequences of GUX, DUF579, RWA and TBL proteins used for phylogenetic reconstruction.Table S1 Arabidopsis, Eucalyptus and Populus genes potentially involved in xylan modification and cumulative evidence for naming of xylan modification genes in Populus and Eucalyptus. Table S2 Confirmed Arabidopsis SCW xylan modification genes and probable homologs in Eucalyptus. Table S3 Eucalyptus grandis query genes used for the co‐expression analysis and the subset that are probable xylan modification genes.Table S4 1112 genes co‐expressed with 24 xylan modification genes. Table S5 Functional enrichment and annotation of genes present in the five expression modules produced by the co‐expression algorithm.Table S6 Expression module genes corresponding to GO, KEGG and MM terms. Table S7 Eucalyptus grandis query genes which passed criteria set during co‐expression analysis, membership to an expression module and correlation with SCW associated genes.Table S8 Identification of bins significantly enriched in trans‐eQTLs.Table S9 Xylem expressed genes affected by seven hotspots.Table S10 Overlap of hotspot loci identified in this study with previously identified global hotspots.Table S11 Core set genes corresponding to enriched terms for GO, Kegg and MapMan.Table S12 Genes corresponding to process categories on systems model.Table S13 All genes affected by seven hotspot loci.Table S14 Genes corresponding to numbered reaction steps on Fig. S13.Table S15 Genes corresponding to numbered reaction steps on Fig. 3 as well as the genes missing from Fig. 3, indicated on Fig. S14.Table S16 Genes linked to acetyl‐CoA production corresponding to the numbered reaction steps on Fig. 5 as well as the genes missing from Fig. 5, indicated on Fig. S15.Table S17 Examples of how the systems model can be used as a tool to design and test new biotechnology approaches to alter cell wall structure and chemistry.The National Research Foundation (NRF) of South Africa – Bioinformatics and Functional Genomics Programme (BFG Grant UID 86936 and 97911), the Technology and Human Resources for Industry Programme (THRIP Grant UID 80118 and 96413), the Department of Science and Technology (Strategic Grant for the Eucalyptus Genomics Platform) and by Sappi Forest Research through the Forest Molecular Genetics Programme at the University of Pretoria. MPW, NC and DP acknowledge postgraduate and postdoctoral scholarship support from the NRF.http://www.newphytologist.com2020-09-01hj2019BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis

Background: Carbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink. Results: Here, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production. Conclusions: CAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.Botany, Department ofForestry, Faculty ofScience, Faculty ofWood Science, Department ofNon UBCReviewedFacult

The genome of Eucalyptus grandis

International audienceEucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology