Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology
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Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. / de Flamingh, Alida; Ishida, Yasuko; Pečnerová, Patrícia; Vilchis, Sahara; Siegismund, Hans R.; van Aarde, Rudi J.; Malhi, Ripan S.; Roca, Alfred L.
I: Frontiers in Genetics, Bind 13, 1021004, 2023.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology
AU - de Flamingh, Alida
AU - Ishida, Yasuko
AU - Pečnerová, Patrícia
AU - Vilchis, Sahara
AU - Siegismund, Hans R.
AU - van Aarde, Rudi J.
AU - Malhi, Ripan S.
AU - Roca, Alfred L.
N1 - Publisher Copyright: Copyright © 2023 de Flamingh, Ishida, Pečnerová, Vilchis, Siegismund, van Aarde, Malhi and Roca.
PY - 2023
Y1 - 2023
N2 - Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
AB - Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
KW - endangered species
KW - fecal DNA
KW - L. africana
KW - metagenomic analysis
KW - molecular pipeline
KW - nuclear genome
U2 - 10.3389/fgene.2022.1021004
DO - 10.3389/fgene.2022.1021004
M3 - Journal article
C2 - 36712847
AN - SCOPUS:85147030169
VL - 13
JO - Frontiers in Genetics
JF - Frontiers in Genetics
SN - 1664-8021
M1 - 1021004
ER -
ID: 335022618