Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy

Expression Analysis of TCP Transcription Factor Family in Autopolyploids of Chrysanthemum nankingense

Autopolyploids often exhibit plant characteristics different from their diploid ancestors and are frequently associated with altered genes expression controlling growth and development. TCP is a unique transcription factor family in plants that is closely related to plant growth and development. Based on transcriptome sequencing of Chrysanthemum nankingense, 23 full-length TCP genes were cloned. The expression of CnTCP9 was most variable in tetraploids, at least threefold greater than diploids. Due to the lack of a C. nankingense transgenic system, we overexpressed CnTCP9 in Arabidopsis thaliana (Col-0) and Chrysanthemum morifolium. Overexpression of CnTCP9 caused enlargement of leaves in A. thaliana and petals in C. morifolium, and the expression of genes downstream of the GA pathway in C. morifolium were increased. Our results suggest that autopolyploidization of C. nankingense led to differential expression of TCP family genes, thereby affecting plant characteristics by the GA pathway. This study improves the understanding of enlarged plant size after autopolyploidization.

An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae)

Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.

Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense×Tanacetum vulgare hybrid and allopolyploid (Asteraceae)

Allopolyploid formation involves two major events: interspecific hybridization and polyploidization. A number of species in the Asteraceae family are polyploids because of frequent hybridization. The effects of hybridization on genomics and transcriptomics in Chrysanthemum nankingense×Tanacetum vulgare hybrids have been reported. In this study, we obtained allopolyploids by applying a colchicine treatment to a synthesized C. nankingense×T. vulgare hybrid. Sequence-related amplified polymorphism (SRAP), methylation-sensitive amplification polymorphism (MSAP), and high-throughput RNA sequencing (RNA-Seq) technologies were used to investigate the genomic, epigenetic, and transcriptomic alterations in both the hybrid and allopolyploids. The genomic alterations in the hybrid and allopolyploids mainly involved the loss of parental fragments and the gain of novel fragments. The DNA methylation level of the hybrid was reduced by hybridization but was restored somewhat after polyploidization. There were more significant differences in gene expression between the hybrid/allopolyploid and the paternal parent than between the hybrid/allopolyploid and the maternal parent. Most differentially expressed genes (DEGs) showed down-regulation in the hybrid/allopolyploid relative to the parents. Among the non-additive genes, transgressive patterns appeared to be dominant, especially repression patterns. Maternal expression dominance was observed specifically for down-regulated genes. Many methylase and methyltransferase genes showed differential expression between the hybrid and parents and between the allopolyploid and parents. Our data indicate that hybridization may be a major factor affecting genomic and transcriptomic changes in newly formed allopolyploids. The formation of allopolyploids may not simply be the sum of hybridization and polyploidization changes but also may be influenced by the interaction between these processes.