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. The rubber tree (Hevea brasiliensis, hereafter referred to as Hevea) is a member of the spurge family (Euphorbiaceae), along with several other economically important species such as cassava (Manihot esculenta) and the castor oil plant (Ricinus communis). Natural rubber (cis-1, 4-polyisoprene) makes up about one-third of the volume of latex that is essentially cytoplasm of the articulated laticifers in Hevea. The latex is extracted by tapping the bark, a non-destructive method of harvesting that facilitates continual production. As an industrial commodity, natural rubber is an elastomer with physical and chemical properties that cannot be fully matched by synthetic rubber1. In contrast to synthetics, the production of natural rubber is sustainable and environment friendly2. The commercial cultivation of Hevea, a native to the Amazon Basin, began in 1896 on a plantation scale in Malaya (now Malaysia) and expanded to other Southeast Asian countries that lead in world natural rubber production today3. Decades of selective breeding have resulted in a gradual improvement in rubber productivity, from 650 kg ha–1 derived from unselected seedlings during the 1920s to 2,500 kg ha–1 yielded by elite cultivars by the 1990s4. Nevertheless, the field production achieved so far is still well below the theoretical yield of 7,000–12,000 kg ha–1, as has been suggested for the rubber tree5. Meanwhile, conventional rubber breeding has been stagnating in the introduction of high-yield cultivars. The reasons include a narrow genetic basis for exploiting breeding potential and difficulty in introducing wild germplasms because of the genetic burden in removing unfavourable alleles6. The incorporation of marker-assisted selection and transgenic techniques offers promise to improve breeding efficiency for latex yield, and sequencing of the Hevea genome would uncover even more avenues leading to this end. The first draft Hevea genome was released by a Malaysian team7 that was participant to the recent boom in transcriptomic and proteomic studies of the species8,9,10,11. However, its low sequence coverage (∼13×) and a lack of large insert libraries (such as fosmid- or BAC-based clone libraries) have limited the success of genome assembly (a scaffold N50 size of 2,972 bp), precluding its application for furthering quality research in the field. Here, we report a high-quality genome assembly of Hevea Reyan7-33-97, an elite cultivar widely planted in China12,13 based on sequence data from both whole-genome shotgun (WGS) and pooled BAC clones. This assembly contains 7,453 scaffolds (N50 = 1.28 Mb), has a length of 1.37 Gb and covers ∼94% of the predicted genome size (1.46 Gb). Together with analysis of data from re-sequencing five other cultivars and comprehensive transcriptomic surveys, we aim to obtain new insights into the physiology of laticifers and molecular details of rubber biosynthesis, especially in relation to ethylene-stimulated rubber production. (Résumé d'auteur

Mitochondrial genome and phylogenomic analysis of Pseudo-nitzschia micropora (Bacillariophyceae, Bacillariophyta)

The number of species in the genus Pseudo-nitzschia has increased to 56, including 26 species known to produce domoic acid (DA), which is harmful to marine animals and human health. The lack of genomic sequences of Pseudo-nitzschia species has been a limiting factor in the studies of genetic and evolutionary relationships of Pseudo-nitzschia species. Here, the complete mitochondrial genome sequence of Pseudo-nitzschia micropora was determined for the first time, which was 38,792 bp in length with the overall AT content being 69.98%. The mitochondrial genome encoded 62 genes, including 36 protein-coding genes (PCGs, including orf157), 24 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Phylogenetic tree analysis suggests that the P. micropora had a closer relationship with P. cuspidate than that with P. multiseries. The availability of the complete mitochondrial genome of P. micropora would be useful for researching the evolutionary relationships of Pseudo-nitzschia species

Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

The haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains (four strains obtained in this study, and one strain previously published) revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa.</jats:p