AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat<i>Felis catus</i>of American Shorthair breed

Isobe, Sachiko; Matsumoto, Yuki; Chung, C.Y.; Sakamoto, Mika; Chan, Ting‐Fung; Hirakawa, Hideki; Ishihara, Genki; Lam, Hon‐Ming; Nakayama, Shinobu; Sasamoto, Shigemi; Tanizawa, Yasuhiro; Watanabe, Akïharu; Watanabe, Kei; Yagura, Masaru; Nakamura, Yasukazu

doi:10.1101/2020.05.19.103788

Cited by 5 publications

(8 citation statements)

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“…2), which may reflect differences in numt copy number and sequence. To understand the possible influence of numt sequences in tissue types where mixed nuclear and mitochondrial sequences might occur, we mined three available long-read cat genome assemblies ( [39,40]; Bioproject PRJNA773801) and also analysed sequence variation in numt arrays via long-amplicon Nanopore sequencing.…”

Section: Discussionmentioning

confidence: 99%

“…3a). The third assembly (AnAms1.0) derived from 'Senzu', an American shorthair cat [40], includes a partial numt array containing flanking DNA on one side only and 15 near full-length copies of the numt repeat followed by a final truncated inverted copy of the numt (~3 kb) carrying the same internal deletion as Fca-508 (Fig. 3a).…”

Section: Structures and Diversity Of Numt Sequencesmentioning

confidence: 99%

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Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

Patterson

Lall

Neumann

et al. 2023

Preprint

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Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct mitotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the test was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common mitotype at the control region. The random match probability (RMP) in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.

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Section: Discussionmentioning

confidence: 99%

Section: Structures and Diversity Of Numt Sequencesmentioning

confidence: 99%

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

Patterson

Lall

Neumann

et al. 2023

Preprint

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“…Low‐quality reads (phred score < 30), adapter sequences, and reads with lengths <20 nucleotides were removed using fastp v.0.22.0 20 . The quality‐filtered reads were mapped and aligned to 2 genome assemblies of domestic cats with different origins (Felis_catus_9.0 [felCat9] from an Abyssinian cat named Cinnamon 21 and AnAms1.0 from an American Shorthair cat named Senzu 22 ) by Dynamic Read Analysis for GENomics (DRAGEN v4.0.3; Illumina Inc.). DRAGEN provided a gVCF file using the enable‐map‐align option.…”

Section: Methodsmentioning

confidence: 99%

“…SnpEff v.5.1d with default settings was used for annotation 24 . We used felCat9 in Ensembl v.105 and built for AnAms1.0 with in‐house scripts in the Cats‐I database (v. r1.0.2) 22 . We denoted candidate causative variants as those that passed hard filtering of DRAGEN analyses and exhibited high‐, moderate‐, and low‐impact predictions in SnpEff.…”

Section: Methodsmentioning

confidence: 99%

A de novo nonsense variant in the DMD gene associated with X‐linked dystrophin‐deficient muscular dystrophy in a cat

Yokoyama,

Matsumoto,

Yamaguchi

et al. 2024

Veterinary Internal Medicne

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BackgroundX‐linked dystrophin‐deficient muscular dystrophy (MD) is a form of MD caused by variants in the DMD gene. It is a fatal disease characterized by progressive weakness and degeneration of skeletal muscles.Hypothesis/ObjectivesIdentify deleterious genetic variants in DMD by whole‐genome sequencing (WGS) using a next‐generation sequencer.AnimalsOne MD‐affected cat, its parents, and 354 cats from a breeding colony.MethodsWe compared the WGS data of the affected cat with data available in the National Center for Biotechnology Information database and searched for candidate high‐impact variants by in silico analyses. Next, we confirmed the candidate variants by Sanger sequencing using samples from the parents and cats from the breeding colony. We used 2 genome assemblies, the standard felCat9 (from an Abyssinian cat) and the novel AnAms1.0 (from an American Shorthair cat), to evaluate genome assembly differences.ResultsWe found 2 novel high‐impact variants: a 1‐bp deletion in felCat9 and an identical nonsense variant in felCat9 and AnAms1.0. Whole genome and Sanger sequencing validation showed that the deletion in felCat9 was a false positive because of misassembly. Among the 357 cats, the nonsense variant was only found in the affected cat, which indicated it was a de novo variant.Conclusion and Clinical ImportanceWe identified a de novo variant in the affected cat and next‐generation sequencing‐based genotyping of the whole DMD gene was determined to be necessary for affected cats because the parents of the affected cat did not have the risk variant.

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“…Significant hurdles remain in the quest to deliver genomic medicine to cats and other companion animals: annotations that depict RNA isoforms are sparse; National Center for Biotechnology Information (NCBI) and ENSEMBL gene models often conflict; noncoding epigenetic features are lacking; Y chromosome assemblies are incomplete [ 14 , 15 ]; and the sequence contents of nucleolar organizer regions, telomeres, and centromeres are undefined. As more conspecific assemblies are produced [ 16 ], how will we integrate their information?…”

mentioning

confidence: 99%

The ninth life of the cat reference genome, Felis_catus

Zhang

Schoenebeck

2020

PLoS Genet

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AnAms1.0: A high-quality chromosome-scale assembly of a domestic catFelis catusof American Shorthair breed

Cited by 5 publications

References 35 publications

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing

A de novo nonsense variant in the DMD gene associated with X‐linked dystrophin‐deficient muscular dystrophy in a cat

The ninth life of the cat reference genome, Felis_catus

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