Whole-transcriptome profiles of Chrysanthemum seticuspe improve genome annotation and shed new light on mRNA-miRNA-lncRNA networks in ray florets and disc florets

BACKGROUND

Chrysanthemum seticuspe has emerged as a model plant species of cultivated chrysanthemums, especially for studies involving diploid and self-compatible pure lines (Gojo-0). Its genome was sequenced and assembled into chromosomes. However, the genome annotation of C. seticuspe still needs to be improved to elucidate the complex regulatory networks in this species.

RESULTS

In addition to the 74,259 mRNAs annotated in the C. seticuspe genome, we identified 18,265 novel mRNAs, 51,425 novel lncRNAs, 501 novel miRNAs and 22,065 novel siRNAs. Two C-class genes and YABBY family genes were highly expressed in disc florets, while B-class genes were highly expressed in ray florets. A WGCNA was performed to identify the hub lncRNAs and mRNAs in ray floret- and disc floret-specific modules, and CDM19, BBX22, HTH, HSP70 and several lncRNAs were identified. ceRNA and lncNAT networks related to flower development were also constructed, and we found a latent functional lncNAT-mRNA combination, LXLOC_026470 and MIF2.

CONCLUSIONS

The annotations of mRNAs, lncRNAs and small RNAs in the C. seticuspe genome have been improved. The expression profiles of flower development-related genes, ceRNA networks and lncNAT networks were identified, laying a foundation for elucidating the regulatory mechanisms underlying disc floret and ray floret formation.

PIN and PILS family genes analyses in Chrysanthemum seticuspe reveal their potential functions in flower bud development and drought stress

Auxin affects almost all plant growth and developmental processes. The PIN-FORMED (PIN) and PIN-LIKES (PILS) family genes determine the direction and distribution gradient of auxin flow by polar localization on the cell membrane. However, there are no systematic studies on PIN and PILS family genes in chrysanthemum. Here, 18 PIN and 13 PILS genes were identified in Chrysanthemum seticuspe. The evolutionary relationships, physicochemical properties, conserved motifs, cis-acting elements, chromosome localization, collinearity, and expression characteristics of these genes were analyzed. CsPIN10a, CsPIN10b, and CsPIN10c are unique PIN genes in C. seticuspe. Expression pattern analysis showed that these genes had different tissue specificities, and the expression levels of CsPIN8, CsPINS1, CsPILS6, and CsPILS10 were linearly related to the developmental period of the flower buds. In situ hybridization assay showed that CsPIN1a, CsPIN1b, and CsPILS8 were expressed in floret primordia and petal tips, and CsPIN1a was specifically expressed in the middle of the bract primordia, which might regulate lateral expansion of the bracts. CsPIN and CsPILS family genes are also involved in drought stress responses. This study provides theoretical support for the cultivation of new varieties with attractive flower forms and high drought tolerance.

De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis

Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C. seticuspe accession developed by five generations of self-crossing from a self-compatible strain, AEV2, was used for genome sequencing. The 2.72 Gb of assembled sequences (CSE_r1.0), consisting of 354,212 scaffolds, covered 89.0% of the 3.06 Gb C. seticuspe genome estimated by k-mer analysis. The N50 length of scaffolds was 44,741 bp. For protein-encoding genes, 71,057 annotated genes were deduced (CSE_r1.1_cds). Next, based on the assembled genome sequences, we performed linkage map construction, gene discovery and comparative analyses for C. seticuspe and cultivated chrysanthemum. The generated C. seticuspe linkage map revealed skewed regions in segregation on the AEV2 genome. In gene discovery analysis, candidate flowering-related genes were newly found in CSE_r1.1_cds. Moreover, single nucleotide polymorphism identification and annotation on the C. × morifolium genome showed that the C. seticuspe genome was applicable to genetic analysis in cultivated chrysanthemums. The genome sequences assembled herein are expected to contribute to future chrysanthemum studies. In addition, our approach demonstrated the usefulness of short-read genome assembly and the importance of choosing an appropriate next genome sequencing technology based on the purpose of the post-genome analysis.