Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis

• Main Authors: Duncan Kiragu Gichuki, Lu Ma, Zhenfei Zhu, Chang Du, Qingyun Li, Guangwan Hu, Zhixiang Zhong, Honglin Li, Qingfeng Wang, Haiping Xin
• Format: Article
• Language: English
• Published: PeerJ Inc. 2019-12-01
• Series: PeerJ
• Subjects: Cissus quadrangularis; Genome size; Copia; Repeat elements; Chromosome counts; Gypsy
• Online Access: https://peerj.com/articles/8201.pdf

Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.