De novo assembly and annotation of Asiatic lion (<i>Panthera leo persica</i>) genome

Ara, Sreenivas; Sowpati, Divya Tej; Kumar, Amitha Sampat; Awasthi, Gowri; Kumar, Madan; Tabusum, Wajeeda; Gaur, Ajay

doi:10.1101/549790

Cited by 2 publications

(5 citation statements)

References 53 publications

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“…The lower contig scores are also emulated through a higher number of missing BUSCOs ( Table 2, Supplementary Table S4). Although we were unable to compare it to the de novo assembly of the Asiatic lion from Mitra et al (2019), they report a scaffold N50 of approximately 20kb, suggesting our assembly represents significant improvement.…”

Section: Introductionmentioning

confidence: 79%

“…Minimum depth cutoffs of 10 and maximum depth cutoffs of 100 were applied to all genomes using vcfutils.In order to visualize the PSMC graphs, we applied a mutation rates of 0.9e-09 [56] and a generation time of five years for the lion. We compared these inferences with those from two previously resequenced lions [56] and the Asiatic lion [38]. Table S10: Heterozygosity (observed) from various Panthera individuals when mapped to their own genome compared to when mapped to the domestic cat.…”

Section: Demographic Historymentioning

confidence: 99%

“…To date, no de novo genome assembly for an African lion exists and only two individuals have been resequenced (Cho et al (2013). A de novo assembly of an Asiatic lion was recently completed [38], but was limited to short-read technology, and was thus highly fragmented. Asiatic and African lions are currently regarded as separate subspecies [1,6,39], and we regard them as such for these analyses.…”

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confidence: 99%

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Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Armstrong

Taylor

Miller

et al. 2019

Preprint

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The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly for the captive African lion from the Exotic Feline Rescue Center as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length and levels of homozygosity across the genomes of the lion sequenced here and other previous published resequence data, indicating contrasting histories of recent and ancient small population sizes and/or inbreeding. Demographic analyses reveal similar histories across all individuals except the Asiatic lion, which shows a more rapid decline in population size. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion. using the domestic cat or tiger as a reference [18]. Felid karyotypes are thought to be highly conserved [19,20], but studies have shown a reference mapping bias for estimation of statistics such as heterozygosity [21] and accurate allele calling [22], both of which are important for assessing population history.The causes of the decline in lions are multifactorial. Lions have been hunted by humans for thousands of years, possibly first as a direct competitor and threat to our survival [23], for initiation rituals and rites of passage (e.g. [24][25][26]), to reduce predation of domesticated animals, and more recently for sport [27][28][29][30]. The recent rise of illegal trade in lion parts and illicit breeding practices has escalated over the past ten years, bringing hunting practices and international laws into the spotlight. In addition, several documentaries have exposed the lion breeding industry within South Africa, which uses fenced lions for 'petting', canned hunting experiences, and ultimately as skeletons for export, likely destined for Asian medicines [31]. Accurate and rapid genotyping could aid law enforcement to reveal whether the origins of trafficked goods are from wild or captive populations.Moreover, rapid population decline has put lions at the forefront of the conservation debate over translocations and how best to manage populations. Many efforts to restore previous populations have focused on translocation lions within and between various South African lion populations (e.g. [32,33]. Information about local population adaptation, deleterious alleles, and potential inbreeding is lacking, which further complicates managed relocations. While increasing genetic diversity remains a widely accepted conservation goal...

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Section: Introductionmentioning

confidence: 79%

Section: Demographic Historymentioning

confidence: 99%

mentioning

confidence: 99%

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Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Armstrong

Taylor

Miller

et al. 2019

Preprint

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show abstract

“…In order to visualize the PSMC graphs, we applied a mutation rate of 0.5e−08 [38] and a generation time of 5 years for the lion [38]. We compared these inferences with those from two previously resequenced lions [38] and the Asiatic lion [39]. We additionally tested a generation time of 6 years because there have been contrasting estimates of generation time for lions (see https://www.…”

Section: Demographic Historymentioning

confidence: 99%

“…To date, no de novo genome assembly for an African lion exists and only two individuals' genomes have been resequenced [38]. A de novo assembly of an Asiatic lion was recently completed [39], but as it was limited to short-read technology, is highly fragmented. Asiatic and African lions are currently regarded as separate subspecies [1,6,40], and we regard them as such for these analyses.…”

Section: Introductionmentioning

confidence: 99%

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

et al. 2020

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Background: The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. Results: Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore longread data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. Conclusions:We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

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De novo assembly and annotation of Asiatic lion (Panthera leo persica) genome

Cited by 2 publications

References 53 publications

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

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