4.3 Article

A chromosome-scale high-contiguity genome assembly of the cheetah (Acinonyx jubatus)

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

Stefan Prost et al.

Summary: Cheetahs, as apex predators, play important roles in ecosystems, but they are facing a precarious conservation status due to habitat loss, human-wildlife conflict, and illegal trafficking. A comprehensive genome-wide analysis of cheetah phylogeography revealed that their genetic differentiation is more complex than previously thought, with distinct genetic characteristics in East African cheetahs compared to Southern African cheetahs. Inbreeding was observed in critically endangered Iranian and Northwestern subspecies, and cheetahs were found to have the lowest genome-wide heterozygosity among big cats. These findings provide valuable information for evidence-based conservation policy decisions and protecting this species in light of ongoing translocations and the threat of illegal trafficking.

MOLECULAR ECOLOGY (2022)

Article Evolutionary Biology

Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis)

Kevin R. Bredemeyer et al.

Summary: This study utilized the genomes of domestic cats and Asian leopard cats for genetic analysis, improving the resolution of complex and highly repetitive regions. The new genome assemblies showed significant enhancements in contiguity and capture of chromosome data, providing valuable resources for studies on feline precision medicine, adaptation, and speciation.

JOURNAL OF HEREDITY (2021)

Article Multidisciplinary Sciences

Towards complete and error-free genome assemblies of all vertebrate species

Arang Rhie et al.

Summary: The Vertebrate Genome Project and the international Genome 10K consortium have collaborated to generate high-quality genome assemblies for 16 species representing six major vertebrate lineages, leading to new biological discoveries. Long-read sequencing technologies are essential for maximizing genome quality, and addressing complex repeats and haplotype heterozygosity are crucial for reducing assembly errors and improving completeness of reference genomes. The lessons learned from this project have paved the way for the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all known vertebrate species.

NATURE (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern

Jana Wold et al.

Summary: Structural variants (SVs) are large rearrangements within the genome that impact gene function, and their study offers conservation genomics an exciting opportunity to enhance species recovery by complementing traditional approaches. Despite their potential influence on fitness traits, SVs remain understudied in conservation genomics.

MOLECULAR ECOLOGY (2021)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Biotechnology & Applied Microbiology

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Arang Rhie et al.

GENOME BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Jian-Jun Jin et al.

GENOME BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

Review Genetics & Heredity

The Value of Reference Genomes in the Conservation of Threatened Species

Parice Brandies et al.

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

Jens Keilwagen et al.

BMC BIOINFORMATICS (2018)

Article Multidisciplinary Sciences

The global decline of cheetah Acinonyx jubatus and what it means for conservation

Sarah M. Durant et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Letter Biotechnology & Applied Microbiology

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

Martin Steinegger et al.

NATURE BIOTECHNOLOGY (2017)

Article Biochemical Research Methods

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

Konstantin Okonechnikov et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

Using intron position conservation for homology-based gene prediction

Jens Keilwagen et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Neva C. Durand et al.

CELL SYSTEMS (2016)

Article Genetics & Heredity

Repbase Update, a database of repetitive elements in eukaryotic genomes

Weidong Bao et al.

MOBILE DNA (2015)

Article Biotechnology & Applied Microbiology

Genomic legacy of the African cheetah, Acinonyx jubatus

Pavel Dobrynin et al.

GENOME BIOLOGY (2015)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

InterProScan: protein domains identifier

E Quevillon et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemical Research Methods

A greedy algorithm for aligning DNA sequences

Z Zhang et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2000)