Ricinus communis v1

Abstract

Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiation, strong light, and extremely dry condition. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence assembly of the wild castor accession WT05, with a genome size of 316 Mb, a scaffold N50 of 31.93 Mb, and a contig N50 of 8.96 Mb, respectively. Compared with cultivated castor and other Euphorbiaceae species, the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis, and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.

Genome Information

Sequencing, assembly and annotation

Wild castor WT05 collected from Kenya, Africa was cultivated in the Wuhan botanical garden, Wuhan, China. The sampling details were as follows. Young fresh leaves were first harvested and deposited in liquid nitrogen for genomic DNA extraction. Then, high-quality genomic DNA was extracted using Plant Genomic DNA Kit (Qiagen, San Diego, CA). The extracted high-quality genomic DNA was divided into two parts, one for short-read sequencing on the Illumina NovaSeq 6000 platform and the other for long-read sequencing on the GridION X5 platform with libraries of 20 kb insert size based on Oxford Nanopore technology. We also sampled the RNA-seq materials from the leaves, roots, seeds, and stems of wild castor and extracted total RNA using the QIAGEN RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). In addition, samples for Hi-C library construction were collected from the same plants and sequenced through the Illumina HiSeq platform.

We performed genome assembly with a combination of long Nanopore reads, Illumina short reads, and Hi-C sequencing data. Sequence corrections were performed using Canu (v1.7) [67] with default parameters. Corrected sequences were assembled using SMARTdenovo (https://github.com/ruanjue/smartdenovo) with default parameters (Table S30). Then, the assembled genome was corrected by nanopolish with parameters (-t 4 --min-candidate-frequency 0.05) (https://github.com/jts/nanopolish.git, v0.9.2) using the long-read sequences and polished (five rounds) by pilon (v1.21) using the short-read sequences to finally generate high-quality consensus contigs with default parameters (Figure S18). Finally, Hi-C data help to anchor contigs into ten chromosome-level scaffolds base on the 3D-DNA program (v180922) [68] with the parameters “-r 2 --mode haploid” and the Juicer pipeline (v1.5.7) [69] with the parameters “-s DpnII”. Then, juicerbox was used for genome visualization and manual correction.

Reference Publication(s)

Lu J et al., "A Chromosome-level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert.", Genomics Proteomics Bioinformatics, 2022 Feb;20(1):42-59DOI: 10.1016/j.gpb.2021.04.003