Genome of South African dwarf chameleons decoded

Genome of South African dwarf chameleons decoded

by Alex Laube Science

After a reference genome for the panther chameleon (Furcifer pardalis) was recently published for the first time in China, scientists from South Africa have now followed with the genome of two dwarf chameleon species.

For the analyses, a male Bradypodion pumilum from Cape Town and a male Bradypodion ventrale from an introduced population in Johannesburg were taken. Muscle and liver tissue was used for long sequencing (HiC). The genome size of Bradypodion pumilum is 2.43 gigabase pairs (Gb), that of Bradypodion ventrale 2.40 Gb. The BUSCO analysis demonstrated a high completeness with about 97% of all existing coding genes in vertebrates. Furthermore, the current publication confirms the six macrochromosomes already found from the karyotype in Bradypodion thamnobates 2017. Various comparisons with Anolis sagrei were made. It remains open which chromosomes in Bradypodion are sex chromosomes.

The genomes can be viewed in the NCBI BioProject under the number PRJNA9861319 and under the BioSample numbers SAMN35825189 and SAMN35825190 respectively.

De novo whole genome assemblies for two Southern African Dwarf Chameleons (Bradypodion, Chamaeleonidae)
Jody M. Taft, Krystal A. Tolley, Graham J. Alexander, Anthony J. Geneva
Genome Biology and Evolution 15 (10), 2023, pp. 1-8
DOI: 10.1093/gbe/evad182

Genome of the panther chameleon decoded

Genome of the panther chameleon decoded

by Alex Laube Science

In recent decades, genetic research has developed rapidly. Since 2009, the so-called high fidelity (HiFi) Pacbio sequencing method has been available for sequencing genomes. Nevertheless, relatively little is being done in the reptile field. There are only about a hundred so-called reference genomes for reptiles, and none at all for chameleons. Scientists from China have now published a reference genome for the panther chameleon (Furcifer pardalis).

For the analysis, a 5-year-old male captive panther chameleon was killed using isoflurane and then dissected. Different tissues were frozen in liquid nitrogen. Skeletal muscle was used for short genome DNA sequencing and HI-C sequencing. Liver was used for HiFi sequencing. RNA from heart, liver, spleen, testis, lung, kidney, and skin were used for transcriptome sequencing.

The genome size of the panther chameleon from the K-mer analysis is 1.61 gigabase pairs (Gbp), containing only 22 so-called contigs, sets of overlapping DNA. The karyotype contains 11 chromosomes, each consisting of one to four contigs. Ten out of eleven chromosomes have repeat sequences (TAACCC). BUSCO analysis demonstrated a high completeness of the genome. The genome can be viewed in the NCBI BioProject under the number PRJNA974816 and in ScienceDataBank.

Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome
Hongxin Xie, Zixuan Chen, Shuai Pang, Weiguo Du
Genome Biology and Evolution 131, 2023
DOI: 10.1093/gbe/evad131

 

Picture: Alex Laube