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High-quality genome assembly of an important biodiesel plant, Euphorbia lathyris L.

ABSTRACT: Caper spurge, Euphorbia lathyris L., is an important energy crop and medicinal crop. Here, we generated a high-quality, chromosome-level genome assembly of caper spurge using Oxford Nanopore sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼988.9 Mb in size, 99.8% of which could be grouped into 10 pseudochromosomes, with contig and scaffold N50 values of 32.6 and 95.7 Mb, respectively. A total of 651.4 Mb repetitive sequences and 36,342 protein-coding genes were predicted in the genome assembly. Comparative genomic analysis showed that caper spurge and castor bean clustered together. We found that no independent whole-genome duplication event had occurred in caper spurge after its split from the castor bean, and recent substantial amplification of long terminal repeat retrotransposons has contributed significantly to its genome expansion. Furthermore, based on gene homology searching, we identified a number of candidate genes involved in the biosynthesis of fatty acids and triacylglycerols. The reference genome presented here will be highly useful for the further study of the genetics, genomics, and breeding of this high-value crop, as well as for evolutionary studies of spurge family and angiosperms.

SUBMITTER: Wang M

PROVIDER: S-EPMC8545615 | biostudies-literature |

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of <i>Euphorbia lathyris</i> L. (Euphorbiaceae).

Project description:Euphorbia lathyris L. is a well-known bioenergy plant cultivated in many parts of the world. In this study, we sequenced the complete chloroplast (cp) genome sequence of E. lathyris to investigate its phylogenetic relationship in the family Euphorbiaceae. The cp genome was 163,738 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,837 bp) separated by a large single-copy region (LSC: 91,783 bp) and a small single-copy region (SSC: 18,281 bp). The GC content of whole cp genome is 35.6%. Annotation showed the presence of 113 unique genes with 79 protein-coding genes, four tRNA genes, and 30 rRNA genes. Phylogenetic analysis indicated that E. lathyris was in the basal position of subgen. Esula, closely related to sect. Esula and sect. Helioscopiae.

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Euphorbia factor L(8): a diterpenoid from the seeds of Euphorbia lathyris.

Project description:THE TITLE COMPOUND [SYSTEMATIC NAME: (2S*,3S*,4R*,5R*,9S*,11S*,15R*)-5,15-diacet-oxy-3-nicotino-yloxy-14-oxolathyra-6(17),12(E)-diene], C(30)H(37)NO(7), was isolated from the seeds of Euphorbia lathyris. The tricyclic diterpenoid molecule contains an 11-membered ring, a five-membered ring exhibiting an envelope conformation and a three-membered ring. The 11-membered ring is cis-fused with the three-membered ring and trans-fused with the five-membered ring.

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High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Project description:Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 Mb and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence, and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and Salvia miltiorrhiza was estimated at 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing, and comparative genomics among related species.

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Distinct triterpene synthases in the laticifers of Euphorbia lathyris.

Project description:Euphorbia lathyris was proposed about fifty years ago as a potential agroenergetic crop. The tremendous amounts of triterpenes present in its latex has driven investigations for transforming this particular biological fluid into an industrial hydrocarbon source. The huge accumulation of terpenes in the latex of many plant species represent a challenging question regarding cellular homeostasis. In fact, the enzymes, the mechanisms and the controllers that tune the amount of products accumulated in specialized compartments (to fulfill ecological roles) or deposited at important sites (as essential factors) are not known. Here, we have isolated oxidosqualene cyclases highly expressed in the latex of Euphorbia lathyris. This triterpene biosynthetic machinery is made of distinct paralogous enzymes responsible for the massive accumulation of steroidal and non-steroidal tetracyclic triterpenes. More than eighty years after the isolation of butyrospermol from shea butter (Heilbronn IM, Moffet GL, and Spring FS J. Chem. Soc. 1934, 1583), a butyrospermol synthase is characterized in this work using yeast and in folia heterologous expression assays.

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Characterization of the complete chloroplast genome of <i>Euphorbia lathyris</i> (Euphorbiaceae), a traditional Chinese medicine.

Project description:Euphorbia lathyris is a biennial herb plant in China. The seed is commonly used in well-known traditional Chinese medicine, and it has anti-tumor, p-glycoprotein and tyrosinase inhibitory activities. The length of circular chloroplast genome was 162,571 bp, containing a large single-copy region of 91,946 bp, a small single-copy region of 17,301 bp and two inverted repeat regions of 26,662 bp. The chloroplast genome contained 128 genes, including 85 protein-coding, 8 rRNA, and 35 tRNA genes. Phylogenetic tree analysis showed that E. lathyris, E. kansui and E. esulaare are closely related to each other.

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A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes.

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