scholarly journals Ultracontinuous single haplotype genome assemblies for the domestic cat (Felis catus) and Asian leopard cat (Prionailurus bengalensis)

2020 ◽  
Author(s):  
Kevin R Bredemeyer ◽  
Andrew J Harris ◽  
Gang Li ◽  
Le Zhao ◽  
Nicole M Foley ◽  
...  
Keyword(s):  
De Novo ◽  
Companion Animals ◽  
Felis Catus ◽  
Domestic Cat ◽  
Illumina Sequence ◽  
Primary Reference ◽  
Genomic Studies ◽  
Leopard Cat ◽  
Prionailurus Bengalensis ◽  
Genome Assemblies

Abstract In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the two species’ haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in one or two large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation and speciation.

scholarly journals AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed

2020 ◽  
Author(s):  
Sachiko Isobe ◽  
Yuki Matsumoto ◽  
Claire Chung ◽  
Mika Sakamoto ◽  
Ting-Fung Chan ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Companion Animals ◽  
Felis Catus ◽  
Domestic Cat ◽  
Genome Database ◽  
Genomic Resources ◽  
Genomic Technologies ◽  
Long Read ◽  
Limited Power ◽  
Genome Assemblies

AbstractThe domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat, Felis catus genome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and ab initio gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

310 NUCLEAR AND MICROTUBULE REMODELING AND IN VITRO DEVELOPMENT OF NUCLEAR TRANSFERRED CAT OOCYTES WITH SKIN FIBROBLASTS OF DOMESTIC CAT AND LEOPARD CAT

2006 ◽  
Vol 18 (2) ◽  
pp. 262 ◽  
Author(s):  
X. J. Yin ◽  
E. G. Choi ◽  
S. J. Cho ◽  
J. Y. Jin ◽  
N. H. Kim ◽  
...  
Keyword(s):  
Nuclear Transfer ◽  
Statistical Significance ◽  
Domestic Cat ◽  
Developmental Potential ◽  
Decondensed Chromatin ◽  
Leopard Cat ◽  
Prionailurus Bengalensis ◽  
Microtubule Aster ◽  
Vitro Development

The leopard cat (Prionailurus bengalensis), a member of the felidae family, is a threatened animal in South Korea. In terms of endangered felids, nuclear transfer is a potentially valuable technique for assuring the continuation of species with dwindling numbers. The protocol for nuclear transfer has been described previously (Yin et al. 2005 Reproduction 129, 245-249). In this experiment we evaluated nuclear and microtubule remodeling and the in vitro developmental potential of enucleated cat oocytes reconstructed with nuclei from either domestic cat fibroblasts (DCF) or leopard cat fibroblasts (LCF). Microtubule aster was allocated to decondensed chromatin at 6 h post-activation following nuclear transfer of fibroblast cells from both DCF and LCF (3/3 in DCF, 2/3 in LCF), suggesting the introduction of a somatic cell centrosome (Kim et al. 1996 Mol. Reprod. Dev. 43, 248-255; Park et al. 2004 Mol. Reprod. Dev. 68, 25-34). At 12 h following nuclear transfer, the nucleus swelled into a large pronucleus-like structure in most reconstructed oocytes (5/9 in DCF and 4/6 in LCF), which showed further enlargement until 18 h after nuclear transfer (4/6 in DCF, 4/6 in LCF). Two microtubule asters were seen near the swollen nucleus. At 18 h following nuclear transfer, the mitotic metaphase (1/6 in DCF) or two cell divisions (1/6 in DCF, 2/6 in LCF) were observed. The percentage of blastocyst formation from nuclear transfer embryos derived from DCF (4/46, 8.6%) was not significantly different from that for nuclear transfer embryos constructed with LCF (4/52, 7.6%). Statistical significance was established at the P < 0.05 level by a X2-test (SAS; SAS Institute, Inc., Cary, NC, USA). These results indicate that nuclear and microtubule remodeling processes and in vitro developmental ability are similar in cat oocytes reconstructed with both domestic cat and leopard cat nuclei. This work was supported by KOSEF (grant # M10525010001-05N2501-00110).

scholarly journals Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1375
Author(s):  
Hideyuki Ito ◽  
Nobuyoshi Nakajima ◽  
Manabu Onuma ◽  
Miho Murayama
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
De Novo ◽  
Draft Genome ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Domestic Cat ◽  
Ex Situ ◽  
Genetic Management ◽  
Leopard Cat

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

scholarly journals Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

2020 ◽  
Author(s):  
Anton Zamyatin ◽  
Pavel Avdeyev ◽  
Jiangtao Liang ◽  
Atashi Sharma ◽  
Chujia Chen ◽  
...  
Keyword(s):  
De Novo ◽  
Mosquito Species ◽  
Sub Saharan Africa ◽  
Malaria Vectors ◽  
Anopheles Coluzzii ◽  
Reference Quality ◽  
Genomic Studies ◽  
Sub Saharan ◽  
Genome Assemblies ◽  
Chromosome Level

AbstractBackgroundAnopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.FindingsIn this study, we produced de novo chromosome-level genome assemblies for An. coluzzii and An. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 265.7 Mbp assemblies for An. coluzzii and An. arabiensis, respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in An. coluzzii and An. arabiensis.ConclusionThe new chromosome-level assemblies will facilitate functional and population genomic studies in An. coluzzii and An. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

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