Draft Genome Assembly for the Tibetan Black Bear (Ursus thibetanus thibetanus)

Zhu, Chenglong; Xu, Wenjie; Li, Jianchuan; Liu, Chang; Hu, Mingliang; Yuan, Yuan; Yuan, Ke; Zhang, Yijiuling; Song, Xingzhi; jinsoo, Han; Cui, Xinxin

doi:10.3389/fgene.2020.00231

Cited by 9 publications

(12 citation statements)

References 43 publications

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“…Moreover, inconsistencies with previous estimates of total N e across species appear to be attributable to differences in the selected mutation rate. Here, we predict a nearly doubled N e compared to previous results (Cahill et al 2013; Kumar et al 2017; Endo et al 2021; Zhu et al 2020; Liu et al 2014; Lan et al 2022), which is consistent with expectations for having a mutation rate that is approximately halved (Nadachowska-Brzyska et al 2016). This mutation rate is likely more accurate since it was calculated directly through trio sequencing (Wang et al 2022).…”

Section: Resultssupporting

confidence: 91%

“…Across most repetitive element classes, a majority of the bears had comparable numbers, but differed most substantially in the total amount of 'Small RNA', 'Unclassified', and 'Other' (comprising satellites, simple repeats, and low complexity regions) (Figure 1b). Consistent with previous results, we found that long interspersed nuclear elements (LINEs) represented the largest percentage of repetitive elements in the Ursidae family (Zhu et al 2020;Srivastava et al 2019), however, one study reported fewer total repeats in the American black bear (Ursus americanus) and a greater number of repeats overall in the giant panda (Ailuropoda melanoleuca) (Srivastava et al 2019). Interestingly, while most Ursid species contain a relatively low percent of small RNA repetitive elements, we find expansions of this repetitive element class in the Andean bear (Tremarctos ornatus) and the Japanese black bear (Ursus thibetanus japonicus) (Figure 1b).…”

Section: Repetitive Contentsupporting

confidence: 92%

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A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

Armstrong

Perry

Huang

et al. 2022

Preprint

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The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully-phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size was 2.47 Megabases (Mb) with a scaffold and contig N50 length of 70.08 and 43.94 Mb, respectively. BUSCO analysis revealed that 94.5% of single-copy orthologs from mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy BUSCOs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.

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Section: Resultssupporting

confidence: 91%

Section: Repetitive Contentsupporting

confidence: 92%

A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

Armstrong

Perry

Huang

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Moreover, inconsistencies with previous estimates of total N e across species appear to be attributable to differences in the selected mutation rate. Here, we predict a nearly doubled N e compared to previous results ( Cahill et al 2013 ; Liu et al 2014 ; Kumar et al 2017 ; Zhu et al 2020 ; Endo et al 2021 ; Lan et al 2022 ), which is consistent with expectations for having a mutation rate that is approximately halved ( Nadachowska-Brzyska et al 2016 ). This mutation rate is likely more accurate since it was calculated directly through trio sequencing (Wang et al 2022).…”

Section: Resultssupporting

confidence: 91%

“…1 B ). Consistent with previous results, we found that long interspersed nuclear elements (LINEs) represented the largest percentage of repetitive elements in the Ursidae family ( Srivastava et al 2019 ; Zhu et al 2020 ), however, one study reported fewer total repeats in the American black bear ( Ursus americanus ) and a greater number of repeats overall in the giant panda ( Ailuropoda melanoleuca ) ( Srivastava et al 2019 ). Interestingly, while most Ursid species contain a relatively low percent of small RNA repetitive elements, we find expansions of this repetitive element class in the Andean bear ( Tremarctos ornatus ) and the Japanese black bear ( Ursus thibetanus japonicus ) ( Fig.…”

Section: Resultssupporting

confidence: 90%

A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos)

Armstrong

Perry

Huang

et al. 2022

Genome Biology and Evolution

View full text Add to dashboard Cite

The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Megabases (Mb), respectively. BUSCO analysis revealed that 94.5% of single copy orthologs from Mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy orthologs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.

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“…Heterozygous sites were extracted by performing Samtools (v1.3.1, Li et al. 2009 ) with the parameters “mpileup -q 20 -Q 20.” Finally, the PSMC model ( Li and Durbin 2011 ) was analyzed using the parameters -N25 -t15 -r5 -b -p “4þ25*2þ4þ6.” ( ZHu et al. 2020 ).…”

Section: Methodsmentioning

confidence: 99%

The First Draft Genome of a Cold-Water Coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae)

Zhou

Feng

et al. 2020

Genome Biology and Evolution

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Cold-water corals (CWCs) are important habitats for creatures in the deep-sea environment, but they have been degraded by anthropogenic activity. So far, no genome for any CWC has been reported. Here, we report a draft genome of Trachythela sp., which represents the first genome of CWCs to date. In total, 56 Gb and 65 Gb of raw reads were generated from Illumina and Nanopore sequencing platforms, respectively. The final assembled genome was 578.26Mb, which consisted of 396 contigs with a contig N50 of 3.56 Mb, and the genome captured 90.1% of the metazoan Benchmarking Universal Single-Copy Orthologs. We identified 335Mb (57.88% of the genome) of repetitive elements, which is a higher proportion compared with others in the Cnidarians, along with 35,305 protein-coding genes. We also detected 483 expanded and 51 contracted gene families, and many of them were associated with longevity, ion transposase, heme-binding nicotinamide adenine dinucleotide, and metabolic regulators of transcription. Overall, we believe this genome will serve as an important resource for studies on community protection for CWCs.

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Draft Genome Assembly for the Tibetan Black Bear (Ursus thibetanus thibetanus)

Cited by 9 publications

References 43 publications

A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos)

A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos)

The First Draft Genome of a Cold-Water Coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae)

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