PMC

Analysis of transcriptome differences between during wild and cultivated Saposhnikovia divaricata in the bolting and non-bolting period. Volcano plots of DEGs (A, B). DEGs in ZW vs. YW (left, A) and ZC vs. YC (right, B). The horizontal coordinate shows the log2FoldChange value, and the vertical coordinate shows the –log10 padj or –log10 P-value. The threshold line for the differential gene screening criteria is represented by a black dashed line. Upregulated genes are shown in red, and downregulated genes are shown in green (A). Cluster dendrogram of differentially expressed genes in wild and cultivated S. divaricata without bolting (B). GO enrichment with DEGs of wild and cultivated S. divaricata with bolting (C). GO enrichment with DEGs without bolting (D). KEGG enrichment with DEGs with bolting (E). KEGG enrichment with DEGs without bolting (F). KEGG enrichment with DEGs with bolting. ZW, cultivated S. divaricata without bolting; YW, wild S. divaricata without bolting; ZC, cultivated S. divaricata with bolting; YC, wild S. divaricata with bolting.

Overview of the Saposhnikovia divaricata genome. A Morphology of S. divaricata. B Hi-C heatmap of S. divaricata chromosome interactions.

Photographs showing the overgrowth of Galaxaura divaricata on a degraded coral reef flat in the lagoon of Dongsha Atoll with three types of coral reef fishes (territorial farming damselfish, juvenile parrotfish, and carnivorous fish that use Galaxaura divaricata as feeding substratum. (a) Territorial farming damselfishes (white arrowheads) defend their territories against intruders across the Galaxaura canopy; (b) farming damselfish Hemiglyphidodon plagiometopon, likely feeding on epiphytes and detritus from the surface of G. divaricata; (c) a group of juvenile parrotfishes including Scarus rivulatus, S. ghobban, S. schlegelii, and Chlorurus spilurus likely feeding on epiphytic microalgae from the surface of G. divaricata. Predators including goatfish, Parupeneus multifasciatus (black arrowhead), and the wrasse Cheilinus chlorourus (white arrowhead) follow a group of roving parrotfish to feed on small invertebrates associated with G. divaricata; (d) the carnivorous wrasse, Stethojulis strigiventer forage for small invertebrates hidden between the branches of G. divaricata; (e) late juvenile or early initial phase Chlorurus spilurus likely grazing on microepiphytes from the surface of G. divaricata.

Functional analysis of differentially expressed genes. (A): DEGs in the roots and leaves of S. divaricata. (B): Cluster heatmap of differentially expressed genes in root and leaf of S. divaricata. (C): Go mapping of differentially expressed genes in root and leaf of S. divaricata.