The rubber tree genome reveals new insights into rubber production and species adaptation.

The Para rubber tree (Hevea brasiliensis) is an economically important tropical tree species that produces natural rubber, an essential industrial raw material. Here we present a high-quality genome assembly of this species (1.37 Gb, scaffold N50 = 1.28 Mb) that covers 93.8% of the genome (1.47 Gb) and harbours 43,792 predicted protein-coding genes. A striking expansion of the REF/SRPP (rubber elongation factor/small rubber particle protein) gene family and its divergence into several laticifer-specific isoforms seem crucial for rubber biosynthesis. The REF/SRPP family has isoforms with sizes similar to or larger than SRPP1 (204 amino acids) in 17 other plants examined, but no isoforms with similar sizes to REF1 (138 amino acids), the predominant molecular variant. A pivotal point in Hevea evolution was the emergence of REF1, which is located on the surface of large rubber particles that account for 93% of rubber in the latex (despite constituting only 6% of total rubber particles, large and small). The stringent control of ethylene synthesis under active ethylene signalling and response in laticifers resolves a longstanding mystery of ethylene stimulation in rubber production. Our study, which includes the re-sequencing of five other Hevea cultivars and extensive RNA-seq data, provides a valuable resource for functional genomics and tools for breeding elite Hevea cultivars.

Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources.

To identify all the gene products involved in cellulosic biomass degradation, we employed RNA sequencing technology to perform a genome-wide comparison of gene expression during growth of Trichoderma reesei QM9414 on cellulose or glucose. Due to their important role in lignocellulose decomposition, we focused on CAZymes and other secreted proteins. In total, 122 CAZymes showed at least a two-fold change in mRNA abundance, and 97 of those were highly induced by cellulose. Compared to the well-characterized cellulases and hemicellulases, a majority of the other upregulated CAZymes showed lower transcriptional levels. In addition, 64 secreted proteins, including oxidoreductases, exhibited at least two-fold upregulation on cellulose medium. To better understand the potential roles of low-abundance CAZymes in cellulose breakdown, we compared the expression patterns of 25 glycoside hydrolase genes under different conditions via real-time PCR. Substantial differences for the 25 genes were observed for individual strains grown on different carbon sources, and between QM9414 and RUTC30 when grown on the same carbon source. Moreover, we identified 3 genes that are coregulated with known cellulases. Collectively, this study highlights a comprehensive transcriptional profile for biomass degradation-related proteins and provides a first step toward the identification of candidates to construct optimized enzyme cocktails.

Metagenomic insights into the fibrolytic microbiome in yak rumen.

The rumen hosts one of the most efficient microbial systems for degrading plant cell walls, yet the predominant cellulolytic proteins and fibrolytic mechanism(s) remain elusive. Here we investigated the cellulolytic microbiome of the yak rumen by using a combination of metagenome-based and bacterial artificial chromosome (BAC)-based functional screening approaches. Totally 223 fibrolytic BAC clones were pyrosequenced and 10,070 ORFs were identified. Among them 150 were annotated as the glycoside hydrolase (GH) genes for fibrolytic proteins, and the majority (69%) of them were clustered or linked with genes encoding related functions. Among the 35 fibrolytic contigs of >10 Kb in length, 25 were derived from Bacteroidetes and four from Firmicutes. Coverage analysis indicated that the fibrolytic genes on most Bacteroidetes-contigs were abundantly represented in the metagenomic sequences, and they were frequently linked with genes encoding SusC/SusD-type outer-membrane proteins. GH5, GH9, and GH10 cellulase/hemicellulase genes were predominant, but no GH48 exocellulase gene was found. Most (85%) of the cellulase and hemicellulase proteins possessed a signal peptide; only a few carried carbohydrate-binding modules, and no cellulosomal domains were detected. These findings suggest that the SucC/SucD-involving mechanism, instead of one based on cellulosomes or the free-enzyme system, serves a major role in lignocellulose degradation in yak rumen. Genes encoding an endoglucanase of a novel GH5 subfamily occurred frequently in the metagenome, and the recombinant proteins encoded by the genes displayed moderate Avicelase in addition to endoglucanase activities, suggesting their important contribution to lignocellulose degradation in the exocellulase-scarce rumen.