Genomic resources for Asian ( Elephas maximus ) and African savannah elephant ( Loxodonta africana ) conservation and health research

2023/05/29 by Natalia A. Prado, Ellie E. Armstrong, Janine L. Brown +5 · 1 voice · 1 citation
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Animal Disease Management and Epidemiology #Animal Genetics and Reproduction #Genetic and phenotypic traits in livestock

paper · pdf · doi:10.1093/jhered/esad034

openalex publication_date 2023/05/29 · openalex created_date 2023/05/30 · openalex updated_date 2026/08/04

Abstract

We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.

Citations

• Sinking the Flagship: the Case of Forest Elephants in Asia and Africa
• Clusters of Multiple Mutations: Incidence and Molecular Mechanisms
• Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants
• RepeatModeler2 for automated genomic discovery of transposable element families
• Twelve years of SAMtools and BCFtools
• YaHS: yet another Hi-C scaffolding tool
• Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

Cited by

• Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees

Discussions

• And of course, check out her and coauthors' JHered Genome Resources article from earlier this year sharing new resources for Asian and African elephants! doi.org/10.1093/jher... [bsky, 0 points, 0 comments]