First, we identified the polyploidization events of Solanaceae species and displayed the peak map of the synonymous nucleotide substitution rate in the database. Second, the ancestral karyotype and chromosome evolution footprint map of Solanaceae species were deduced and plotted.
Analysis methods:
| Part | Methods |
|---|---|
| Ks curve | The MUSCLE tool was used for homologous amino acid sequence comparisons (-maxiters 1 -diags -sv -distance1 kbit20-3)[1]. The PAL2NAL program was subsequently used to convert protein comparisons to codon comparisons based on CDSs[2]. Finally, Ka and Ks were calculated using the yn00 program of PAML and the Nei–Gojobori method, respectively[3]. The median Ks value between homologous genes in colined blocks was used to categorize blocks caused by duplication events. The Ks values between colined gene pairs are displayed as a dot plot generated using the “-bk” parameter in the WGDI[4], with different Ks value intervals corresponding to different colors. The distribution of Ks density was determined using three modules of the WGDI: Kspeak (kp), PeaksFit (pf), and KsFigures (kf). Ks density distribution curves were plotted using Kspeak. Multipeak fitting was then performed using PeaksFit. Finally, the multiple fitted density curves were converted into a single plot using Ks figures. |
| Karyotype evolution | We compared the genomes of Solanaceae species and coffee plants (GCA_900059795.1) using homologous gene dot maps and deduced the evolutionary trajectory of Solanaceae from ancestral chromosomes to existing chromosomes according to previous reports(Wang et al. 2015; Wang et al. 2022b). The genetic model proposed in previous studies suggests that the existing chromosomes of relatively new nodes are derived from the fusion of ancestral chromosomes, such as the end-to-end joining (EEJ) of two different chromosomes and the nested chromosome fusion (NCF) of one chromosome inserted into another chromosome(Wang et al. 2015; Zhuang et al. 2019; Song et al. 2021). These two changes not only led to a decrease in the number of chromosomes but also involved gene loss. |