The EMBL-EBI bioinformatics web and programmatic tools framework

Li, Weizhong; Cowley, Andrew Peter; Uludağ, Mahmut; Gur, Tamer; McWilliam, Hamish; Squizzato, Silvano; Park, Young Mi; Buso, Nicola; López, Rodrigo

doi:10.1093/nar/gkv279

Cited by 920 publications

(762 citation statements)

References 39 publications

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“…arabidopsis.org/ index.jsp). The retrieved A. thaliana proteins were processed with Interproscan 65 and Blastp searched against Hevea proteins. Hits sharing >30% amino acid identity and >50% amino acid alignment length with the A. thaliana homologues were further checked for pfam domain architecture.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2016

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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.

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Section: Methodsmentioning

confidence: 99%

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

et al. 2016

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“…8, A and B) and exists in solution as a dimer with a predicted size of 93 kDa (Fig. 8C) (61)(62)(63), and the tree was generated using Dendroscope (64).…”

Section: Identification Of Udp-apiose Synthase Homologs In Avascularmentioning

confidence: 99%

Functional Characterization of UDP-apiose Synthases from Bryophytes and Green Algae Provides Insight into the Appearance of Apiose-containing Glycans during Plant Evolution

Smith

Yang

Levy³

et al. 2016

Journal of Biological Chemistry

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Apiose is a branched monosaccharide that is present in the cell wall pectic polysaccharides rhamnogalacturonan II and apiogalacturonan and in numerous plant secondary metabolites. These apiose-containing glycans are synthesized using UDPapiose as the donor. UDP-apiose (UDP-Api) together with UDPxylose is formed from UDP-glucuronic acid (UDP-GlcA) by UDP-Api synthase (UAS). It was hypothesized that the ability to form Api distinguishes vascular plants from the avascular plants and green algae. UAS from several dicotyledonous plants has been characterized; however, it is not known if avascular plants or green algae produce this enzyme. Here we report the identification and functional characterization of UAS homologs from avascular plants (mosses, liverwort, and hornwort), from streptophyte green algae, and from a monocot (duckweed). The recombinant UAS homologs all form UDP-Api from UDP-glucuronic acid albeit in different amounts. Apiose was detected in aqueous methanolic extracts of these plants. Apiose was detected in duckweed cell walls but not in the walls of the avascular plants and algae. Overexpressing duckweed UAS in the moss Physcomitrella patens led to an increase in the amounts of aqueous methanol-acetonitrile-soluble apiose but did not result in discernible amounts of cell wall-associated apiose. Thus, bryophytes and algae likely lack the glycosyltransferase machinery required to synthesize apiose-containing cell wall glycans. Nevertheless, these plants may have the ability to form apiosylated secondary metabolites. Our data are the first to provide evidence that the ability to form apiose existed prior to the appearance of rhamnogalacturonan II and apiogalacturonan and provide new insights into the evolution of apiose-containing glycans.

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“…3A). The 1,108-amino acid GH31 protein encoded by Kfla_4052, designated Kfla4052, shares 79.0% similarity (with 0.4% gaps; calculated using the EMBOSS Water pairwise sequence alignment tool (12)) with the IMT of A. globisformis A19. The 948-amino acid protein encoded by Kfla_4051, designated Kfla4051, shares high (78.3%) sequence similarity with the GH31 protein 6-GT of A. globisformis A19.…”

Section: Resultsmentioning

confidence: 99%

Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1→6)-α-nigerosyl

Tagami¹,

Miyano²,

Sadahiro³

et al. 2016

Journal of Biological Chemistry

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The EMBL-EBI bioinformatics web and programmatic tools framework

Cited by 920 publications

References 39 publications

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

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

Functional Characterization of UDP-apiose Synthases from Bryophytes and Green Algae Provides Insight into the Appearance of Apiose-containing Glycans during Plant Evolution

Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1→6)-α-nigerosyl

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