Cost-effective assembly of the African wild dog (<i>Lycaon pictus</i>) genome using linked reads

Armstrong, Ellie E.; Taylor, Ryan W.; Prost, Stefan; Blinston, Peter; Meer, Esther van der; Madzikanda, Hillary; Mufute, Olivia; Mandisodza‐Chikerema, Roseline; Stuelpnagel, John; Sillero‐Zubiri, Claudio; Petrov, Dmitri A.

doi:10.1093/gigascience/giy124

Cited by 22 publications

(21 citation statements)

References 62 publications

(103 reference statements)

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“…Linked-read, long-read, and long-range scaffolding genomic technologies such as 10x Genomics, Nanopore, and Hi-C allow rapid and economical de novo construction of high-quality and highly contiguous genomes (e.g., [59]). Projects such as Genome 10k [60,61], i5k [62], DNA Zoo (dnazoo.org [50,51];), and Bird 10k [63] aim to vastly improve our general understanding of the evolution of genomes, and both the origin and fate of diversity of life on Earth.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Long and linked-read genomic technologies such as 10x Genomics, Nanopore, and Hi-C allow rapid and economical de novo construction of high quality and highly contiguous genomes (e.g. [71]). Projects such as Genome 10k [72,73], i5k [74], DNAzoo (DNAzoo.org; [57,58]), and bird10k [75] aim to vastly improve our general understanding of the evolution of genomes, and both the origin and fate of diversity of life on earth.…”

Section: Discussionmentioning

confidence: 99%

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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“…With the rapid evolution of genome sequencing technologies over the past decade, whole genome sequences could be obtained in a more economical and efficient way (Weisenfeld et al, 2017;Paajanen et al, 2019). For example, the high-quality reference genomes of the African wild dog (Lycaon pictus) were generated at a low cost by using the linked-read 10× Genomics Chromium system (Armstrong Taylor et al, 2019). However, to date, there is still no genome assembly information publicly available for bar-headed geese.…”

Section: Introductionmentioning

confidence: 99%

First de novo whole genome sequencing and assembly of the bar-headed goose

Wang

Hao

et al. 2020

PeerJ

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Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

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Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads

Cited by 22 publications

References 62 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

First de novo whole genome sequencing and assembly of the bar-headed goose

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