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. 2022 Dec 6:10:e14428.
doi: 10.7717/peerj.14428. eCollection 2022.

Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica

J Antonio Baeza  1   2   3
Affiliations

Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica

J Antonio Baeza. PeerJ. .

Abstract

The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.

Keywords: Endangered species; Metagenome; Mitochondrial genomes; eDNA.

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Conflict of interest statement

The author declares that they have no competing interests.

Figures

Figure 1
Figure 1. Bioinformatics pipeline to assemble the mitochondrial genome of Panthera tigris altaica from scat eDNA samples.
Figure 2
Figure 2. Circular DNA mitochondrial genome map of Panthera tigris altaica assembled from eDNA scat (sample SRR7429863).
The annotated map depicts 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS: 12 S ribosomal RNA and rrnL: 16 S ribosomal RNA), 22 transfer RNA (tRNA) genes, and the putative control region (not annotated). Photo credit: Tuxyso/Wikimedia Commons, CC BY-SA 3.0. https://commons.wikimedia.org/w/index.php?curid=22692001.
Figure 3
Figure 3. Mitophylogenomics of the genus Panthera.
Phylogenetic analysis of Panthera tigris altaica scat samples, conspecifics, and related congeneric species in the subfamily Pantherinae. Total evidence phylogenetic tree obtained from ML analysis based on a concatenated alignment of amino acids of the 13 protein-coding genes present in the mitochondrial genome of representatives of the subfamily Pantherinae. In the analysis, one species of the subfamily Felinae was used as outgroup. Numbers above or below the branches represent bootstrap values.
See this image and copyright information in PMC

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