The aim of the present study was to investigate the photosynthetic properties and transcriptomic profiles of wildtype and chlorophyll (Chl) blacking rice (Oryza sativa L.). The plastid ultrastructure of the Chl blacking rice (i.e., loss of starch granules, abundant vesicles, and abundant plastoglobuli) indicated abnormal plastid development, whereas the analysis of transcriptome profiles and differentially expressed genes revealed that gene encoding PsbR (PSII core protein) was downregulated in the mutant, thereby reducing the Chl accumulation of the mutant. Meanwhile, in regards to Chl biosynthesis and degradation pathways, GluTR gene was downregulated, whereas UROD, CPOX, and MgCH genes were upregulated. The qPCR results were generally consistent with those of the transcription analysis, except for the finding that NOL genes, which regulate Chl b degradation, were upregulated. These results suggest that both the reduction in Chl accumulation and increase in conversion rate of Chl b to Chl a caused Chl a/b ratio amplification in mutant. The present study also provides evidence for Chl b degradation via pheophorbide b.

Photosynthetic properties and transcriptomic profiles of green and white sectors of Ficus microcarpa (c.v. milky stripe fig) leaves were examined in naturally variegated plants. An anatomic analysis indicated that chloroplasts of the white sectors contained a higher abundance of starch granules and lacked stacked thylakoids. Moreover, no photosynthetic rate was detected in the white sectors. Transcriptome profile and differential expressed gene (DEG) analysis showed that genes encoding PSII core proteins were down-regulated in the white sectors. In genes related to chlorophyll metabolism, no DEGs were identified in the biosynthesis pathway of chlorophyll. However, genes encoding the first step of chlorophyll breakdown were up-regulated. The repression of genes involved in N-assimilation suggests that the white sectors were deprived of N. The mutation in the transcription factor mitochondrial transcription termination factor (mTERF) suggests that it induces colorlessness in leaves of the milky stripe fig.

Photosynthesis is an essential biological process and a key approach for raising crop yield. However, photosynthesis in rice is not fully investigated. This study reported the photosynthetic properties and transcriptomic profiles of chlorophyll (Chl) b-deficient mutant (ch11) and wild-type rice (Oryza sativa L.). Chl b-deficient rice revealed irregular chloroplast development (indistinct membranes, loss of starch granules, thinner grana, and numerous plastoglobuli). Next-generation sequencing approach application revealed that the differential expressed genes were related to photosynthesis machinery, Chl-biosynthesis, and degradation pathway in ch11. Two genes encoding PsbR (PSII core protein), FtsZ1, and PetH genes, were found to be down-regulated. The expression of the FtsZ1 and PetH genes resulted in disrupted chloroplast cell division and electron flow, respectively, consequently reducing Chl accumulation and the photosynthetic capacity of Chl b-deficient rice. Furthermore, this study found the up-regulated expression of the GluRS gene, whereas the POR gene was down-regulated in the Chl biosynthesis and degradation pathways. The results obtained from RT-qPCR analyses were generally consistent with those of transcription analysis, with the exception of the finding that MgCH genes were up-regulated which enhance the important intermediate products in the Mg branch of Chl biosynthesis. These results indicate a reduction in the accumulation of both Chl a and Chl b. This study suggested that a decline in Chl accumulation is caused by irregular chloroplast formation and down-regulation of POR genes; and Chl b might be degraded via the pheophorbide b pathway, which requires further elucidation.

Photosynthetic and transcriptomic characteristics of a chlorophyll (Chl) b-deficient mutant type 2b rice (ch14) were investigated in this study. The ultrastructure of chloroplast in ch14 demonstrated irregular chloroplast enhancement (loss of starch granules, indistinct membranes, and thinner grana). Ch14 had significantly lower carotenoid, Chl a, Chl b, and total Chl contents, but a higher ratio of Chl a to Chl b than a wide-type rice. 3,594 genes were differentially expressed in ch14, among which 309 transcription factors were related to Chl degradation and biosynthesis, chloroplast formations, and the photosynthesis capacity. PsbR, GSA-AT, PBGD, PPOX, MgMT, and POR genes were down-regulated, reducing Chl content and photosynthetic capacity in the ch14. This study suggests that Chl degradation may be attributed to abnormal chloroplast development and down-regulation of gene expression in the common pathway and Mg branch and the rise in Chl a to Chl b ratio may be involved in the alternative Chl b degradation pathway.

Terpios hoshinota is a ferocious, space-competing sponge that kills a variety of stony corals by overgrowth. Outbreaks of this species have led to intense coral reef damage and declines in living corals on the square kilometer scale in many geographical locations. Our large-scale 16S rRNA metagenome study across three oceans revealed that the core microbiome of T. hoshinota included OTUs related to Prochloron, Endozoicomonas, Pseudospirillum, SAR116, Magnetospira, and Ruegeria. A Prochloron-like OTU was the most dominant cyanobacterium in T. hoshinota in the western Pacific Ocean, South China Sea, and Indian Ocean. The high-quality draft genome of the Prochloron-like cyanobacterium and our pigment analysis revealed that, unlike the previously described Prochloron species and their genomes, this bacterium had phycobiliproteins and phycobilins and lacked chlorophyll b. Furthermore, the phylogenetic analyses demonstrated that the bacterium was phylogenetically distinct to Prochloron, strongly suggesting that it should be a sister taxon to Prochloron; we therefore proposed this symbiotic cyanobacterium as a novel species under a new genus: Candidatus Prochlorobium terpiosii. In addition, we also characterize the metabolic potentials of the cyanobacterium in carbon and nitrogen cycling and propose a model for the interaction between Ca. Pb. terpiosii LD05 and T. hoshinota. This study builds the foundation for T. hoshinota's microbiome and paves a way for understanding the ecosystem, invasion mechanism, and causes of outbreak of this coral-killing sponge.