Whole genome approach in conservation biology and its perspectives

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Abstract

Conservation biology aims to maintain biological diversity and to defend species from extinction. The number of endangered species is constantly increasing from year to year, reflecting both a deteriorating situation and an increasing number of studied species. In order to obtain a reliable assessment of the status and conservation planning of threatened species, not only an estimate of current total abundance, but also data on population structure, demographic history, and genetic diversity are needed. The development of new approaches and lower costs of sequencing have made it possible to solve these problems at a level previously inaccessible and have led to the formation of conservation genomics. This review discusses the opportunities and prospects offered by the use of whole genome sequencing in conservation biology, features of sample gathering for sequencing, as well as some features of planning whole genome studies. In addition, emphasis is placed on the importance of the formation of open biobanks of samples and cell cultures at the national level.

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Sergei F. Kliver

Institute for Molecular and Cellular Biology SB RAS

Author for correspondence.
Email: mahajrod@gmail.com
ORCID iD: 0000-0002-2965-3617
SPIN-code: 8635-4259
Scopus Author ID: 56449314300
ResearcherId: E-9613-2015

researcher

Russian Federation, 8/2, Academika Lavrentieva str., Novosibirsk, 630090

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Supplementary files

Supplementary Files
Action
1. Fig. 1. Dynamics for the number of endangered species, divided into various categories of Red List. This is based on previously published data [2]

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2. Fig. 2. Tasks of conservation biology, solved by genetic, and bioinformatics methods

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3. Fig. 3. Examples of heterozygosity visualization. а – a graph for total ROH length at different cutoff thresholds along the length for lions from different populations; b – heterozygosity of individuals of Sacharian oryx from different populations. The points on the graph correspond to the average level of heterozygosity for each chromosome separately; c – histogram for the number of heterozygous and homozygous variants reported for two subspecies of the sable antelope (Hippotragus niger). SB2027* and HN216* – individuals belonging to the southern subspecies (H. n. Niger), while the rest belong to Zambian subspecies (H. n. Kirkii); d – average level of heterozygosity and total length of ROH observed for the genomes of wolves of the Isle Royal Island population; e – average heterozygosity in sliding windows for giant otter and two subspecies of sea otter, northern and southern. Original images are from [12, 16, 20, 21, 24]

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4. Fig. 4. Distribution of genome size for 540 mammalian species, from the Animal Genome Size Database [86]. For species with multiple subspecies or dimensions, median value was used

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5. Fig. 5. The number of vertebrate species (Vertebrata) for which chromosome level genome assemblies were published and their coverage of vertebrate taxa: а – overlap by species between the three main databases of chromosomal assemblies; b – representation of vertebrate taxa in these databases. *Sauropsida including birds (Aves)

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