A Chromosome-Level Genome Assembly of Wild Castor Provides New Insights into its Adaptive Evolution in Tropical Desert

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.

Genetic diversity analysis among 123 accessions of castor (Ricinus communis L.) using SSR marker and its association to agronomic traits

“…SSR markers were created in this work using the sequences from gene families with varied expressions in dwarf and high-stalk castor and Jatropha plants (Hu et al 2017;Shi et al 2018;Feng et al 2019). Jatropha curcas and Ricinus communis share high sequence similarities and gene families (Hu et al 2017;Lu et al 2021). The SSR markers from the coding region can produce marker-trait association efficiently (Izzah et al 2016).…”

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…We wished to include as many orders as possible in our study, ideally with access to at least six genomes with high quality, preferably chromosome-level, assemblies, distributed among at least three different families. At the time of data collection, we could obtain suitable data from three fabid orders, Fagales [20][21][22][23][24][25][26][27] (CoGe IDs: 28205, 35079, 51680, 60890-60894, 61298), Cucurbitales [28][29][30][31][32][33] (CoGe IDs: 51412, 52000, 52078, 52080, 52081, 52083, 52084) and Malpighiales [34][35][36][37][38][39] (CoGe IDs: 16772, 60439, 63100, 63108-63110); three malvid orders, Myrtales [40][41][42][43][44] The phylogenies we used for the rosid orders appear in Fig. 8, those for the asterids in Fig.…”

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

“…We wished to include as many orders as possible in our study, ideally with access to at least six genomes with high quality, preferably chromosome-level, assemblies, distributed among at least three different families. At the time of data collection, we could obtain suitable data from three fabid orders, Fagales [20–27], Cucurbitales [28–33], Malpighiales [34–39]; three malvid orders, Myrtales [40–44], Malvales [45–50] and Sapindales [51–61]; one campanulid order, Asterales [62–68]; and three lamiid orders, Gentianales [69–75], Lamiales [76–82] and Solanales [83–88], plus Ericales [89–94]. Other orders with sufficient genomes available were not selected, such as Fabales, because representative genomes from only one or two families were available, or Brassicales, which is the subject of a concurrent publication.…”

“…We wished to include as many orders as possible in our study, ideally with access to at least six genomes with high quality, preferably chromosome-level, assemblies, distributed among at least three different families. At the time of data collection, we could obtain suitable data from three fabid orders, Fagales [20][21][22][23][24][25][26][27], Cucurbitales [28][29][30][31][32][33], Malpighiales [34][35][36][37][38][39]; three malvid orders, Myrtales [40][41][42][43][44], Malvales [45][46][47][48][49][50] and Sapindales [51][52][53][54][55][56][57][58][59][60][61]; one campanulid order, Asterales [62][63][64][65][66]…”