☆ 4.7 Article

Highly accurate long reads are crucial for realizing the potential of biodiversity genomics

BMC GENOMICS (2023)

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 Biotechnology & Applied Microbiology

Telomere-to-telomere assembly of diploid chromosomes with Verkko

Mikko Rautiainen et al.

Summary: The Telomere-to-Telomere consortium has achieved the first complete sequence of a human genome. They used a combination of long Nanopore sequencing reads and high-resolution assembly graph to resolve repeat sequences and automate the process in their Verkko pipeline. The result is a phased, diploid assembly with many chromosomes assembled from end to end. This advance is crucial for constructing comprehensive pangenome databases and chromosome-scale comparative genomics.

NATURE BIOTECHNOLOGY (2023)

添加到收藏夹

Review Biochemistry & Molecular Biology

Pathways to polar adaptation in fishes revealed by long-read sequencing

Scott Hotaling et al.

Summary: This study utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, and compared it to other Antarctic fishes. The study revealed unique evolution and adaptation features in O. amberensis and highlighted the importance of long-read sequencing in understanding genome evolution.

MOLECULAR ECOLOGY (2022)

添加到收藏夹

Review Biology

The rise of genomics in snake venom research: recent advances and future perspectives

Wei-qiao Rao et al.

Summary: Snake venoms contain bioactive proteins that can be used for drug discovery, and the evolution of snake venom proteins is driven by gene duplication and positive selection. Snake genomics is still in its early stages but has the potential to provide insights into venom evolution and toxinology. The presence of repeat sequences in snake genomes poses challenges for DNA sequencing, but advances in sequencing technologies and computational tools have improved our understanding of snake venom evolution.

GIGASCIENCE (2022)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

Hongyu Duan et al.

Summary: This study presents the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compares the performance of Nanopore MinION and PacBio HiFi sequencing technologies. The study shows that false-positive Hi-C contacts between haplotypes are mainly caused by phase switches.

GENOME BIOLOGY (2022)

添加到收藏夹

Article Evolutionary Biology

Draft Genome Assemblies and Annotations of Agrypnia vestita Walker, and Hesperophylax magnus Banks Reveal Substantial Repetitive Element Expansion in Tube Case-Making Caddisflies (Insecta: Trichoptera)

Lindsey K. Olsen et al.

Summary: Trichoptera (caddisflies) are essential for freshwater ecosystems, with the genetic diversity playing a key role in evolutionary studies. Tube case-making caddisflies have genomes at least three times larger than retreat-making caddisflies, driven in part by expansion of repetitive elements. This suggests caddisflies are a promising model for understanding genome size evolution in diverse insect lineages.

GENOME BIOLOGY AND EVOLUTION (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Toward a genome sequence for every animal: Where are we now?

Scott Hotaling et al.

Summary: The field of animal genome science has rapidly progressed in recent years, with significant taxonomic disparities, overrepresentation of vertebrates, and underrepresentation of arthropods being highlighted. The use of long-read sequencing has greatly improved assembly quality, but gene annotations are still lacking for many taxa. While there is a growing pool of researchers participating in animal genome science globally, institutions in the Global North continue to dominate the field.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

添加到收藏夹

Article Biochemical Research Methods

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

Haoyu Cheng et al.

Summary: hifiasm is a novel assembler that utilizes long high-fidelity sequence reads to accurately represent haplotype information, outperforming existing tools in haplotype-resolved assembly on various datasets, including a hexaploid genome dataset.

NATURE METHODS (2021)

添加到收藏夹

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)

添加到收藏夹

Article Evolutionary Biology

Long Reads Are Revolutionizing 20 Years of Insect Genome Sequencing

Scott Hotaling et al.

Summary: The insect genome research has made significant progress over the past 20 years, but there is still bias in the genome assembly of insect species. Assemblies incorporating long-read sequencing technology are significantly more contiguous than those that do not, and future efforts to build insect genome resources require better integration, balanced sampling, and improved gene annotations.

GENOME BIOLOGY AND EVOLUTION (2021)

添加到收藏夹

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)

添加到收藏夹

Review Genetics & Heredity

Towards population-scale long-read sequencing

Wouter De Coster et al.

Summary: Long-read sequencing technologies have advanced to the point where they can be applied to variant detection at a population scale. New computational tools have led to the emergence of population-scale studies in the past two years, with many more expected in the future. The review covers recent developments, challenges, experimental design guidance, as well as strategies for variant validation and genotyping.

NATURE REVIEWS GENETICS (2021)

添加到收藏夹

Article Plant Sciences

Representation and participation across 20 years of plant genome sequencing

Rose A. Marks et al.

Summary: In the past 20 years, the field of plant genome sequencing has grown rapidly, resulting in increased quantity and quality of publicly available genomic resources. However, significant taxonomic gaps exist, and the field has been primarily dominated by affluent nations in the Global North.

NATURE PLANTS (2021)

添加到收藏夹

Article Biochemical Research Methods

Fast and accurate long-read assembly with wtdbg2

Jue Ruan et al.

NATURE METHODS (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Shujun Ou et al.

NATURE COMMUNICATIONS (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Sergey Nurk et al.

GENOME RESEARCH (2020)

添加到收藏夹

Article Biology

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

Dandan Lang et al.

GIGASCIENCE (2020)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

GENOME BIOLOGY (2020)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹

Article Biology

Exploring the underwater silken architectures of caddisworms: comparative silkomics across two caddisfly suborders

Paul B. Frandsen et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2019)

添加到收藏夹

Article Biochemical Research Methods

Long-read sequence and assembly of segmental duplications

Mitchell R. Vollger et al.

NATURE METHODS (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

Evgenia V. Kriventseva et al.

NUCLEIC ACIDS RESEARCH (2019)

添加到收藏夹

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

添加到收藏夹

Article Biology

The genome of an underwater architect, the caddisfly Stenopsyche tienmushanensis Hwang (Insecta: Trichoptera)

Shiqi Luo et al.

GIGASCIENCE (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

添加到收藏夹

Article Biochemical Research Methods

WHATSHAP: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

Murray Patterson et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2015)

添加到收藏夹

Review Evolutionary Biology

A field guide to whole-genome sequencing, assembly and annotation

Robert Ekblom et al.

EVOLUTIONARY APPLICATIONS (2014)

添加到收藏夹

Review Genetics & Heredity

Sequencing depth and coverage: key considerations in genomic analyses

David Sims et al.

NATURE REVIEWS GENETICS (2014)

添加到收藏夹

Article Biochemical Research Methods

The MaSuRCA genome assembler

Aleksey V. Zimin et al.

BIOINFORMATICS (2013)

添加到收藏夹

Article Biochemistry & Molecular Biology

Self-Tensioning Aquatic Caddisfly Silk: Ca2+-Dependent Structure, Strength, and Load Cycle Hysteresis

Nicholas N. Ashton et al.

BIOMACROMOLECULES (2013)

添加到收藏夹

Article Biology

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Keith R. Bradnam et al.

GIGASCIENCE (2013)

添加到收藏夹

Article Biochemical Research Methods

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Matthew Kearse et al.

BIOINFORMATICS (2012)

添加到收藏夹

Article Statistics & Probability

ggplot2

Hadley Wickham

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2011)

添加到收藏夹

Article Biochemistry & Molecular Biology

Conservation of Silk Genes in Trichoptera and Lepidoptera

Naoyuki Yonemura et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

添加到收藏夹

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

添加到收藏夹

Article Biochemistry & Molecular Biology

Fine organization of Bombyx mori fibroin heavy chain gene

CZ Zhou et al.

NUCLEIC ACIDS RESEARCH (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.