Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation

Abstract

The tiger, a poster child for conservation, remains an endangered apex predator. Continued survival and recovery will require a comprehensive understanding of their genetic diversity and the use of such information for population management. A high-quality tiger genome assembly will be an important tool for conservation genetics, especially for the Indian tiger, the most abundant subspecies in the wild. Here, we present high-quality near-chromosomal genome assemblies of a female and a male wild Indian tiger (Panthera tigris tigris). Our assemblies had a scaffold N50 of >140 Mb, with 19 scaffolds, corresponding to the 19 numbered chromosomes, containing 95% of the genome. Our assemblies also enabled detection of longer stretches of runs of homozygosity compared to previous genome assemblies which will improve estimates of genomic inbreeding. Comprehensive genome annotation identified 26,068 protein-coding genes, including several gene families involved in key morphological features such as the teeth, claws, vision, olfaction, taste and body stripes. We also identified 301 microRNAs, 365 small nucleolar RNAs, 632 tRNAs and other noncoding RNA elements, several of which are predicted to regulate key biological pathways that likely contribute to tiger’s apex predatory traits. We identify signatures of positive selection in the tiger genome that are consistent with the Panthera lineage. Our high-quality genome will enable use of non-invasive samples for comprehensive assessment of genetic diversity, thus supporting effective conservation and management of wild tiger populations.

Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation

“…Raw sequencing data (DNA and RNA) and genome assemblies can be accessed at NCBI under BioProject accession numbers PRJNA732096 and PRJNA796358. All supporting data and materials are available in the GigaScience GigaDB database [ 91 ].…”

The year of the tiger and the year of tiger genomes!

“…The genome assemblies presented by Zhang et al ( 2022 ) are some of the best tiger assemblies available so far and comparable even to the domestic cat reference genomes. Three out of six extant tiger subspecies account for a total of six chromosome‐level assemblies (two South China tigers [Wang et al, 2021 ; Zhang et al, 2022 ], two Amur tigers [Zhang et al, 2022 , dnazoo.org ], two Bengal tigers [Shukla et al, 2022 ]). Malayan tigers also have a decent genome assembly (Armstrong et al, 2021 ).…”

“…Malayan tigers also have a decent genome assembly (Armstrong et al, 2021 ). Taken together, these assemblies have already started contributing to understanding not only the evolution of tigers (Armstrong et al, 2021 ; Khan et al, 2021 ; Sagar et al, 2021 ; Shukla et al, 2022 ; Zhang et al, 2022 ) but also how these populations can be sustained into the future (Khan et al, 2021 ; Zhang et al, 2022 ). They allow scientists to develop tools for tiger conservation and management (Khan et al, 2022 , 2020 ; Natesh et al, 2019 ; DNAzoo.org ).…”

“…Genome assemblies of the quality presented in Zhang et al ( 2022 ) are essential for accurate estimates of inbreeding using runs of homozygosity (ROH). Fragmented genome assemblies are unable to detect long ROH reliably (Shukla et al, 2022 ). It is because of the high‐quality assembly Zhang et al ( 2022 ) detected ROH segments, spanning approximately 66% of a chromosome, that were shared across the south china tigers.…”

“…The genome annotations of the genomes and the detection of the loci hosting potential deleterious alleles will help on‐ground conservation efforts soon. With the release of so many tiger genome sequences and assemblies (Shukla et al, 2022 ; Wang et al, 2021 ; Zhang et al, 2022 ), this is truly the year of the tiger genomes. What better way to celebrate the year of the tiger?…”