Figure legends
Figure 1 Characterization of the allotetraploid Orinus kokonorica genome. (A) Morphology of O. kokonorica . 1: Plants in native habitat. 2: Chromosome counts (2n = 40) in an O. kokonorica cell. 3: Plant with leaves, roots and rhizomes. 4: Underground root system. 5: Plant grown in greenhouse. (B) Collinearity within the O. kokonorica genome. Tracks from inside to the outside correspond to 1) gene synteny between chromosomes; 2) gene density; 3) LTR/Gypsy retrotransposons; 4) LTR/Copia retrotransposons; 5) ncRNA density; 6) GC content; 7) Pseudochromosomes of O. kokonorica . (C) Dotplots showing the K s values of homologous genes between the Oko (O. kokonorica ) and Cso (C. songorica ) genomes. (D) Gene synteny between the Oko, Cso and Otho (O. thomaeum ) genomes.
Figure 2 Evolution of the Orinus kokonorica genome. (A) Phylogenetic relationships and divergence times among 16 species. The numbers at nodes represent the divergence times. Gene family expansion (+) and contraction (−) are indicated by red and blue, respectively. (B) Venn diagram of orthologous genes shared among five species, Oko (O. kokonorica ), Cso (C. songorica ), Osa (Oryza sativa ), Otho (O. thomaeum ), Zma (Zea mays ). (C) Distribution of average synonymous substitution levels (K s) between syntenic blocks. (D) Classification of gene duplicate origins in the Oko genome. (E) Gene Ontology (GO) enrichment analysis of the tandem duplicated genes in Oko. Circle color represents -log(FDR) (false discovery rate) in the hypergeometric test corrected using BH (Benjamini and Hochberg) method. Circle size represents the gene count of the GO terms.
Figure 3 Genetic differentiation between O. kokonoricaand C. songorica. (A) Distribution of genetic variations on chromosomes. From top to bottom are SNP, deletion, insertion, duplication and inversion. (B) Summary of expression patterns of the orthologous DEG (differentially expressed genes) pairs inO. kokonorica and C. songorica under cold, drought and heat treatments. (C) Expression patterns of the orthologous DEG pairs inO. kokonorica and C. songorica . Tracks from outside to inside correspond to a) chromosomes; b) DEGs in root under cold treatment; c) DEGs in shoot under cold treatment; d) DEGs in root under heat treatment; e) DEGs in shoot under heat treatment; f) DEGs in root under drought treatment; g) DEGs in shoot under drought treatment; h) DEGs synteny between chromosomes. For b-g, blue color indicates downregulation, red color indicates upregulation.
Figure 4 Structural variations (SVs) of the AMGs betweenO. kokonorica and C. songorica . (A) The maximum likelihood phylogenetic tree of the AMGs identified in O. kokonorica, C. songorica and O. sativa . Red stars represent the 17 AMGs with higher expression (twofold change) in CLs compared with that in CHs in C. songorica . (B) Examples of the four types of SVs detected in the 17 orthologous AMG pairs identified in (A). I) SVs in upstream or downstream regions of genes; II) SVs in gene regions (including both intron and exon); III) Domain gain or lost; IV) gene lost. (C) The detailed SVs in the 17 orthologous AMG pairs between the two species.
Figure 5. Characterization of BOP Genes in O. kokonorica . (A) A phylogenetic tree based on BOP/NPR protein sequences identified in O. kokonorica, C. songorica ,O. sativa and A. thaliana . The NPR genes are shown as outgroup. (B) Collinear gene blocks between O. kokonorica andC. songorica indicate that the BOP family has one more tandem duplicated gene in O. kokonorica . (C) The expression of the BOP genes in five tissues of O. kokonorica . Expression level is indicated by transcripts per million (TPM).
Table 1 Assembly and annotation summary of Orinus kokonorica .