Evolution and Domestication Footprints Uncovered from the Genomes of Coix

Abstract

Coix lacryma-jobi, a plant species closely related to Zea and Sorghum, is an important food and medicinal crop in Asia. However, no reference genome of this species has been reported, and its exact phylogeny within the Andropogoneae remains unresolved. Here, we generated a high-quality genome assembly of coix comprising $1.73 Gb with 44 485 predicted protein-coding genes. We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome, despite its drastic genome expansion ($2.3-fold) due mainly to the activity of transposable elements. Phylogenetic analysis revealed that coix diverged with sorghum $10.41 million years ago, which was $1.49 million years later than the divergence between sorghum and maize. Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars, and suggested that coix experienced a strong genetic bottleneck, resulting in the loss of about half of the genetic diversity during domestication, even though many traits have remained undomesticated. Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage, but also an important resource that will greatly benefit molecular breeding of this important crop.

Complete chloroplast genome sequencing of Job’s tears (Coix L.): genome structure, comparative analysis, and phylogenetic relationships

“…However, genetic information refutes that relationship and instead indicates that Sorghum and Saccharum are more similar to Coix than Zea, which is supported by the karyotyping and repetitive sequence analysis reported by Cai et al (2014). We suspect that a recent whole-genome duplication event occurred in Coix, independent of Zea, and then the original species of C. aquatica and S. bicolor diverged ～ 10.0 million year ago (Liu et al 2020;Guo et al 2020). Our chloroplast genome phylogeny confirmed supports the previous conclusions as well.…”

“…Traditionally, the genus Coix included about 10 species or varieties in the world, while it was classified with 6 ～ 12 species or varieties by different Chinese taxonomic reports (Zhuang et al 1994;Li and Qin 1995;Lu and Zuo 1996). To date, its taxonomy remains controversial, recent efforts have provided insight into the evolutionary relationships and domestication of Coix species with the sequencing and assembly of chromosome genomes of C. lacryma-jobi and C. aquatica (Guo et al 2020;Liu et al 2020). In addition, the complete chloroplast genome of C. lacryma-jobi was obtained by long-fragment PCR amplification and its molecular evolutionary relationships to cereal relatives were also discussed (Leseberg and Duvall 2009;Kang et al 2018).…”

Three Genes Predict Prognosis in Microenvironment of Ovarian Cancer

“…The ClustVis web tool 5 was used to generate heat maps and for clustering ( Metsalu and Vilo, 2015 ). The jvenn software 6 was used to display shared upregulated and downregulated genes between the two score groups ( Bardou et al, 2014 ; Liu et al, 2020 ).…”

A genomic link in China roses: and they all lived prickly but water deficient ever after?

“…Gypsy-to-Copia ratio was one of the lowest values in the sequenced species, suggesting that Copia amplification contributes much more than other TEs to BT genome evolution ( Supplementary Table S11; Supplementary Figure S7) (Bennetzen et al, 2012;Guo et al, 2019;Liu et al, 2019;Shi et al, 2019). In general, TEs displayed an apparently dense distribution in the pericentromeric regions on the chromosomes while inversely correlated with gene density ( Figure 1B).…”