Thuo, D. | Search bioRxiv

bioRxiv2024

The first complete mitochondrial genome of tjakura (Great Desert Skink, Liopholis kintorei)

The complete mitochondrial genome (mitogenome) of the tjaku{square}a, Liopholis kintorei was obtained using next-generation sequencing, making it the first recorded mitogenome of the genus Liopholis and the Tiliquini. The mitogenome is 16,844bp in length with a base composition of A (31.7%), T (24.4%), G (14.6%), and C (29.3%) and a G + C content of 43.9%. The genome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (12S and 16S), and three non-coding fragments, consisting of the putative control region and two mitochondrially encoded heavy strand origin of replication region (OriH). The gene order is identical to that of typical skink mitogenomes. This genomic resource will provide valuable information for genetic studies of this genus and contribute to the growing collection of mitogenomes within the family Scincidae.

genomics↗

bioRxiv2022

Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon

Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: a) allele frequency differentials, minor allele frequency (MAF) profiles, and Wrights Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis (PCA), and discriminant analysis of principal components (DAPC). The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for commercial breeding operations, conservation, and species assignment of this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.

genomics↗