Draft genome sequence of the ricin-producing oilseed castor bean

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Castor bean ( Ricinus communis) is an oil crop that belongs to the spurge (Euphorbiaceae) family. Its seeds are the source of castor oil, used for the production of high-quality lubricants due to its high proportion of the unusual fatty acid ricinoleic acid. Castor bean seeds also produce ricin, a highly toxic ribosome inactivating protein, making castor bean relevant for biosafety. We report here the 4.6X draft genome sequence of castor bean, representing the first reported Euphorbiaceae genome sequence. Our analysis shows that most key castor oil metabolism genes are single-copy while the ricin gene family is larger than previously thought. Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage.

Related collections

Most cited references 41

Record: found
Abstract: found
Article: not found

Is Open Access

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Alberto Casagrande (2007)

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

0 comments Cited 1381 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Ray Ming, Shaobin Hou, Yun Feng … (2008)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

0 comments Cited 329 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

Riccardo Velasco, Andrey Zharkikh, Michela Troggio … (2008)

Background Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.

0 comments Cited 321 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-journal-id): 9604648

Journal ID (pubmed-jr-id): 20305

Journal ID (nlm-ta): Nat Biotechnol

Title: Nature biotechnology

ISSN (Print): 1087-0156

ISSN (Electronic): 1546-1696

Publication date Nihms-submitted: 7 September 2010

Publication date (Electronic): 22 August 2010

Publication date (Print): September 2010

Publication date PMC-release: 1 March 2011

Volume: 28

Issue: 9

Pages: 951-956

Affiliations

[1 ]J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA

[2 ]Institute for Genome Sciences (IGS), University of Maryland School of Medicine, Baltimore, MD 21201, USA

[3 ]Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

[4 ]United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Crop Improvement and Utilization, Albany, CA 94710, USA

[5 ]Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

[6 ]International Institute of Tropical Agriculture, Oyo State, Ibadan, Nigeria

[7 ]Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Universität Göttingen, Göttingen, Germany

[8 ]Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge MA 02141, USA

[9 ]Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

Author notes

Correspondence to: Pablo D. Rabinowicz. Correspondence and requests for materials should be addressed to P.D.R. ( prabinowicz@ 123456som.umaryland.edu )

[10]

These authors contributed equally to this work

Article

Manuscript ID: nihpa226448

DOI: 10.1038/nbt.1674

PMC ID: 2945230

PubMed ID: 20729833

SO-VID: ad3c87f0-9c78-4cbf-bffd-59af218f28f7

License:

Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

History

Funding

Funded by: National Institute of Allergy and Infectious Diseases Extramural Activities : NIAID

Draft genome sequence of the ricin-producing oilseed castor bean

Read this article at

Abstract

Related collections

Genome Engineering using CRISPR

Most cited references 41

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety

Author and article information

Journal

Affiliations

Author notes

Article

History

Funding

Categories

Comments

Comment on this article

Similar content 634

Cited by 158

Most referenced authors 1,348