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Article
Plant Sciences
Fangping Li et al.
Summary: This study presented a chromosome-level, gap-free T2T genome assembly of Rhodomyrtus tomentosa using PacBio and ONT long read sequencing. The assembled genome size was 470.35 Mb with 11 pseudochromosomes, and it contained 33,382 genes and 239.31 Mb of repetitive sequences. Phylogenetic analysis revealed the independent evolution of R. tomentosa and a recent whole-genome duplication event. The study also identified the major compounds of anthocyanins and their synthetic pathways in R. tomentosa and suggested that the coloring and high anthocyanin accumulation in R. tomentosa were determined by the activation of anthocyanin synthesis pathway.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Junyang Yue et al.
Summary: This study reports a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. 'Hongyang'. The integrity and contiguity of this new genome version are markedly improved compared to previous versions. The availability of this gap-free genome lays a solid foundation for genome structure and functional genomics studies, as well as for kiwifruit breeding and improvement.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Anzhen Fu et al.
Summary: This study successfully assembled a high-quality genome of Momordica charantia L. var. abbreviata Ser. (Mca), providing insights into the genetic variations involved in bitter gourd fruit quality and the evolutionary process of bitter gourd. It also contributes to the genetic research of bitter gourd by providing a new genetic resource.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Xiaoya Shi et al.
Summary: Using PacBio HiFi long reads, we have generated a telomere-to-telomere (T2T) gap-free reference genome for the grape cultivar PN40024, which is 69 Mb longer and contains 9018 more annotated genes compared to previous versions. This fully annotated reference genome provides a valuable resource for grapevine genetic studies and breeding programs.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Yuhan Zhou et al.
Summary: This study has successfully assembled and annotated a high-quality, telomere-to-telomere, gap-free genome of Fragaria vesca. It has also revealed the genomic evolution relationship between wild and cultivated strawberry, providing important insights for strawberry genetics and molecular breeding.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Yingzhen Wang et al.
Summary: Actinidia eriantha, a fruit tree with abundant vitamin C and strong disease resistance, has been studied in breeding programs and functional genomics studies. This study successfully obtained haplotype-resolved and gap-free genomes, providing a solid foundation for further research on functional genomics and horticultural traits improvement in kiwifruit.
MOLECULAR HORTICULTURE
(2023)
Article
Biotechnology & Applied Microbiology
Shenghan Gao et al.
Summary: Significant improvements in long-read sequencing technologies have allowed for the exploration of complex genomic areas, such as centromeres, and the introduction of the centromere annotation problem. In this study, a generalizable automatic centromere annotation tool called HiCAT is proposed, which is based on hierarchical tandem repeat mining and aims to decode centromere architecture. HiCAT was applied to various datasets and demonstrated improved annotation continuity and the discovery of additional fine structures, showing its performance and versatility.
Article
Biotechnology & Applied Microbiology
Haoyu Cheng et al.
Summary: This paper presents an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to achieve haplotype-resolved genome assembly from single samples without the need for parent sequencing. The algorithm outperforms existing single-sample assembly pipelines and produces assemblies of similar quality to the best pedigree-based assemblies when applied to human and other vertebrate samples.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Sergey Nurk et al.
Summary: The Telomere-to-Telomere (T2T) Consortium has presented a complete sequence of a human genome, T2T-CHM13, which covers the whole genome except for the Y chromosome. This new sequence includes gapless assemblies, error corrections in previous references, and nearly 200 million base pairs of additional sequence with gene predictions, including protein coding genes. The completion of important regions allows for further studies on genetic variations and functions.
Article
Biochemical Research Methods
Marina Pupke Marone et al.
Summary: This article describes modifications to the TRITEX genome assembly workflow driven by the rise of fast and easy long-read contig assembly in inbred plant genomes and the routine deployment in pangenome projects. New features include the use of dense genetic maps as surrogates or complements, and the introduction of user-editable tables to facilitate the curation of contig placements.
Article
Biotechnology & Applied Microbiology
Michael Alonge et al.
Summary: This study introduces RagTag, a toolset for automating assembly scaffolding and patching, and establishes chromosome-scale reference genomes for tomato genotypes M82 and Sweet-100. This provides convenience for functional genomics and genome editing in tomato.
Article
Biochemical Research Methods
Heng Li
Summary: The latest version of minimap2 v2.22 has made improvements in accurately mapping long reads to highly repetitive regions and in allowing alignments through insertions or deletions up to 100 kb by default, addressing major weaknesses in earlier versions.
Article
Multidisciplinary Sciences
Matthew Naish et al.
Summary: The study used long-read sequencing to assemble the Arabidopsis genome and resolve all five centromeres. It found that centromeres consist of megabase-scale tandemly repeated satellite arrays and are invaded by retrotransposons. The centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.
Letter
Biochemistry & Molecular Biology
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
Jia-Ming Song et al.
Summary: This study reported the assembly and analysis of gap-free reference genome sequences for two elite Oryza sativa rice varieties, providing a global view of the structure and function of rice centromeres. The research found that all rice centromeric regions share conserved centromere-specific satellite motifs, with a higher similarity of CentO repeats within the same chromosome.
Article
Biochemical Research Methods
Tatiana Dvorkina et al.
Article
Plant Sciences
Junyang Yue et al.
HORTICULTURE RESEARCH
(2020)
Review
Oncology
Karen H. Miga
EXPERIMENTAL CELL RESEARCH
(2020)
Review
Cell Biology
Syed Farhan Ahmad et al.
Article
Computer Science, Artificial Intelligence
Zhaodong Hao et al.
PEERJ COMPUTER SCIENCE
(2020)
Article
Biotechnology & Applied Microbiology
Aaron M. Wenger et al.
NATURE BIOTECHNOLOGY
(2019)
Article
Plant Sciences
Haolin Wu et al.
HORTICULTURE RESEARCH
(2019)
Article
Biotechnology & Applied Microbiology
Shujun Ou et al.
Article
Biotechnology & Applied Microbiology
Miten Jain et al.
NATURE BIOTECHNOLOGY
(2018)
Review
Genetics & Heredity
Erwin L. van Dijk et al.
TRENDS IN GENETICS
(2018)
Article
Biochemical Research Methods
Guillaume Marcais et al.
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Genetics & Heredity
Shweta Mehrotra et al.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2014)
Article
Biochemical Research Methods
Limin Fu et al.
Article
Biochemical Research Methods
Christiam Camacho et al.
BMC BIOINFORMATICS
(2009)
Review
Genetics & Heredity
Jianxin Ma et al.
TRENDS IN GENETICS
(2007)
