De novo assembly of the Platycladus orientalis (L.) Franco transcriptome provides insight into the development and pollination mechanism of female cone based on RNA-Seq data

Abstract

For seed-bearing plants, the basis of seed and fruit formation is pollination. The normal progression of pollination is through advances in continuous signal exchange and material transfer, which occur mainly in female reproductive organs; thus, the molecular mechanism of development in female reproductive organs is vital for understanding the principle of pollination. However, molecular biology studies on the development of female cones related to pollination are rare and unclear in gymnosperms, especially in Cupressaceae. In this study, Platycladus orientalis , a monotypic genus within Cupressaceae, was chosen to examine female cone transcriptomes at pre-pollination and pollination stages by Illumina paired-end sequencing technology to de novo sequence six libraries with 3 biological replicates. These libraries were used to construct a P . orientalis transcriptome database containing 71,669 unigenes (4,963 upregulated unigenes and 11,747 downregulated unigenes at the pollination stage) for subsequent analysis. Based on the annotations and expression levels, the functions of differentially expressed unigenes and enriched pathways between the developmental processes of female cones were analysed to detail the preliminary development and pollination mechanism of the female cone. Targeted investigations were specifically performed to determine the elementary mechanism of secretion and functioning of the pollination drop, a vital ovule secretion at the pollination stage. Ultimately, the expression of 15 unigenes selected between two stages were further assessed and confirmed using qRT-PCR, which demonstrated reliable data and significant differences in the expression profiles of key genes. As one of the largest available transcriptomic resources of this species, the database is constructed to prospectively adapt to the physiological and genomic data of woody plants. This work provided the first transcriptome profile of P . orientalis female cones at different developmental stages, and will promote the illumination of the pollination mechanism of P . orientalis , and will serve as the basis for in-depth genomic study in the Cupressaceae family. This initiative will arouse the interest and attention of scholars and pave the way for future studies.

Genome-Wide Tissue-Specific Genes Identification for Novel Tissue-Specific Promoters Discovery in Soybean

“…For seed-specific genes, seven significant enriched GO term, including GO:0004867 (serine-type endopeptidase inhibitor activity), GO:0045735 (nutrient reservoir activity), GO:0002020 (protease binding), GO:0004866 (endopeptidase inhibitor activity), GO:0030414 (peptidase inhibitor activity), GO:0061134 (peptidase regulator activity), and GO:0061135 (endopeptidase regulator activity) were screened out, which all play roles in seed aging [ 90 ], storage proteins [ 91 ], seed germination under salt stress [ 92 ], and different nitrogen levels [ 93 ]. GO:0030570 (pectate lyase activity) and GO:0016837 (carbon-oxygen lyase activity, acting on polysaccharides) had been screened out in the flower-specific genes in the process of pigmentation in the petals [ 94 ], petal abscission [ 95 ], female cone development, and pollination mechanism [ 96 ]. The GO enrichment analysis demonstrated that the predicted tissue-specific genes have unique functions consistent with the tissue they were expressed in, with similar results also declared in a previous study [ 73 ].…”

“…Studies have shown that the promoter region contributed to the agronomic traits of plants [ 100 , 101 , 102 , 103 ]. By using CRISPR-Cas9, promoter editing was successfully applied to crop genetic improvements [ 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 ]. Together with being controlled at the transcriptional level, gene expression was also regulated at the post-transcriptional level, such as methylation [ 108 ].…”