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1. BAT Hi-C maps global chromatin interactions in an efficient and economical way

Author:
Huang, Jie; Jiang, Yongpeng; Zheng, Haonan; Ji, Xiong
Source:
Methods 2020 v.170 pp. 38-47
ISSN:
1046-2023
Subject:
genome,   etc   ; DNA; chromatin; mice;     Show all 4 Subjects
Abstract:
... Chromosome Conformation Capture (3C)-based technologies, such as Hi-C, have represented a significant breakthrough in investigating the structure and function of higher-order genome architecture. However, the mapping of global chromatin interactions remains challenging across many biological conditions due to high background noise and financial constraints, especially for small laboratories. Here, ...
DOI:
10.1016/j.ymeth.2019.08.004

2. Building near-complete plant genomes

Author:
Michael, Todd P; VanBuren, Robert
Source:
Current opinion in plant biology 2020 v.54 pp. 26-33
ISSN:
1369-5266
Subject:
genome; genome assembly,   etc   ; chromosomes; genomics; haplotypes; heterozygosity; polyploidy; transposons;     Show all 8 Subjects
Abstract:
... Plant genomes span several orders of magnitude in size, vary in levels of ploidy and heterozygosity, and contain old and recent bursts of transposable elements, which render them challenging but interesting to assemble. Recent advances in single molecule sequencing and physical mapping technologies have enabled high-quality, chromosome scale assemblies of plant species with increasing complexity a ...
DOI:
10.1016/j.pbi.2019.12.009

3. Unzipping haplotypes in diploid and polyploid genomes

Author:
Zhang, Xingtan; Wu, Ruoxi; Wang, Yibin; Yu, Jiaxin; Tang, Haibao
Source:
Computational and Structural Biotechnology Journal 2020 v.18 pp. 66-72
ISSN:
2001-0370
Subject:
genome; genome assembly,   etc   ; chromosomes; diploidy; evolution; haplotypes; heterosis; heterozygosity; polyploidy;     Show all 9 Subjects
Abstract:
... Diploid genomes consist of two homologous copies of chromosomes with one from each parent while polyploid genomes contain more than two homologous sets of chromosomes. Most of the reference genome assemblies collapsed haplotypes that represent ‘mosaic’ sequences, ignoring allelic variants that may be involved in important cellular and biological functions. Unzipping haplotypes into distinct sets o ...
DOI:
10.1016/j.csbj.2019.11.011
PubMed:
31908732
PubMed Central:
PMC6938933

4. Plant pangenomics: approaches, applications and advancements

Author:
Furaste Danilevicz, Monica; Danilevicz, Monica Furaste; Tay Fernandez, Cassandria Geraldine; Marsh, Jacob Ian; Bayer, Philipp Emanuel; Edwards, David
Source:
Current opinion in plant biology 2020 v.54 pp. 18-25
ISSN:
1369-5266
Subject:
genome,   etc   ; biodiversity; genetic variation; phenotype;     Show all 4 Subjects
Abstract:
... With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene diversity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging ...
DOI:
10.1016/j.pbi.2019.12.005

5. Erratum to: The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes

Author:
Liu, Juan; Wei, Yan; Lu, Yongling; Li, Yangyuling; Chen, Qian; Li, Yan
Source:
The journal of microbiology 2020 v.58 no.4 pp. 340
ISSN:
1225-8873
Subject:
genome,   etc   ; humans; immunostimulants; microbiology; mononuclear leukocytes; oligodeoxyribonucleotides;     Show all 6 Subjects
Abstract:
... In the article by Liu et al. published in Journal of Microbiology 2020; 58, 153–162, 1# The Supplementary data’s consecutive numbers (Supplementary data Fig. S2) on 9ᵗʰ line of 4ᵗʰ paragraph in the section of ‘Discussion.’ on page 160 should be corrected in (Supplementary data Fig. S1). The sentence should have read: The results showed that the nonspecific internalization of T03 had only a slight ...
DOI:
10.1007/s12275-020-9724-0

6. Mitochondrial genomes of four satyrine butterflies and phylogenetic relationships of the family Nymphalidae (Lepidoptera: Papilionoidea)

Author:
Yang, Mingsheng; Song, Lu; Zhou, Lin; Shi, Yuxia; Song, Nan; Zhang, Yalin
Source:
International journal of biological macromolecules 2020 v.145 pp. 272-281
ISSN:
0141-8130
Subject:
mitochondrial genome,   etc   ; Nymphalidae; butterflies; genes; phylogeny;     Show all 5 Subjects
Abstract:
... The complete mitochondrial genomes (mitogenomes) of four Satyrini butterflies are newly determined and comparatively analyzed. These mitogenomes are all circular, double-stranded molecules, with the lengths of 15,194 bp (Minois dryas), 15,232 bp (Ypthima motschulskyi), 15,217 bp (Neope muirheadi) and 15,279 bp (Mycalesis francisca). Gene content and arrangement of newly sequenced mitogenomes are h ...
DOI:
10.1016/j.ijbiomac.2019.12.008

7. Correlation between mouse age and human age in anti-tumor research: Significance and method establishment

Author:
Wang, Shuo; Lai, Xiaoxue; Deng, Yihui; Song, Yanzhi
Source:
Life sciences 2020 v.242 pp. 117242
ISSN:
0024-3205
Subject:
genome,   etc   ; animal models; equations; humans; neoplasms; physiology;     Show all 6 Subjects
Abstract:
... Age is closely related with the occurrence and development of tumors, and with treatment outcomes. To improve the accuracy and rigor of preclinical studies, and to enhance consistency between the preclinical research and the clinical reality, the age of experimental animals used in preclinical studies is important. The mouse genome is 99% identical to the human genome, and mice have similar patter ...
DOI:
10.1016/j.lfs.2019.117242

8. Integration of Flow Cytometry and Single Cell Sequencing

Author:
Andreyev, Dmitry S.; Zybailov, Boris L.
Source:
Trends in biotechnology 2020 v.38 no.2 pp. 133-136
ISSN:
0167-7799
Subject:
genome,   etc   ; flow cytometry; mitochondria; phenotype; transcriptome;     Show all 5 Subjects
Abstract:
... Integrating cytometric analysis of cells, mitochondria, and other polynucleotide-containing biological particles with high-throughput single particle sequencing would provide an ultimate bioanalytical tool, simultaneously assessing phenotype, functionality, genome, and transcriptome of each particle in a large population. Here, we describe how such integration could be performed by adapting existi ...
DOI:
10.1016/j.tibtech.2019.09.002

9. Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing

Author:
Molla, Kutubuddin A.; Yang, Yinong
Source:
Trends in biotechnology 2020 v.38 no.2 pp. 136-141
ISSN:
0167-7799
Subject:
genome,   etc   ; artificial intelligence; gene editing; mutation; prediction;     Show all 5 Subjects
Abstract:
... SpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of mutations, and the predictability of editing outcomes using machine learning models. ...
DOI:
10.1016/j.tibtech.2019.08.002

10. Recent advances in CRISPR/Cas9-mediated knock-ins in mammalian cells

Author:
Banan, Mehdi
Source:
Journal of biotechnology 2020 v.308 pp. 1-9
ISSN:
0168-1656
Subject:
genome,   etc   ; CRISPR-Cas systems; gene editing; mice;     Show all 4 Subjects
Abstract:
... Since its inception, the CRISPR/Cas9 technology has been widely utilized for the targeted insertion of donor DNAs into mammalian genomes. A shortcoming with the earlier knock-in (KI) approaches, however, has been the low efficiency of targeted integrations—especially in primary cells and mouse embryos. Since, a variety of novel strategies have been developed towards improving the KI efficiencies i ...
DOI:
10.1016/j.jbiotec.2019.11.010

11. Methods for comparative ChIA-PET and Hi-C data analysis

Author:
Capurso, Dan; Tang, Zhonghui; Ruan, Yijun
Source:
Methods 2020 v.170 pp. 69-74
ISSN:
1046-2023
Subject:
genome,   etc   ; chromatin; high-throughput nucleotide sequencing;     Show all 3 Subjects
Abstract:
... The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). Th ...
DOI:
10.1016/j.ymeth.2019.09.019

12. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells

Author:
Ramani, Vijay; Deng, Xinxian; Qiu, Ruolan; Lee, Choli; Disteche, Christine M.; Noble, William S.; Shendure, Jay; Duan, Zhijun
Source:
Methods 2020 v.170 pp. 61-68
ISSN:
1046-2023
Subject:
genome,   etc   ; cell cycle; chromatin; mammals; surveys;     Show all 5 Subjects
Abstract:
... The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among i ...
DOI:
10.1016/j.ymeth.2019.09.012
PubMed:
31536770
PubMed Central:
PMC6949367

13. Genome Annotator Light (GAL): A Docker-based package for genome analysis and visualization

Author:
Panda, Arijit; Chaudhari, Narendrakumar M.; Tripathy, Sucheta
Source:
Genomics 2020 v.112 no.1 pp. 127-134
ISSN:
0888-7543
Subject:
genome,   etc   ; databases; genomics; high-throughput nucleotide sequencing;     Show all 4 Subjects
Abstract:
... Next generation sequencing techniques produce enormous data but its analysis and visualization remains a big challenge. To address this, we have developed Genome Annotator Light(GAL), a Docker based package for genome analysis and data visualization. GAL integrated several existing tools and in-house programs inside a Docker Container for systematic analysis and visualization of genomes through we ...
DOI:
10.1016/j.ygeno.2019.03.012

14. Evaluation of real-time nanopore sequencing for Salmonella serotype prediction

Author:
Xu, Feng; Ge, Chongtao; Luo, Hao; Li, Shaoting; Wiedmann, Martin; Deng, Xiangyu; Zhang, Guangtao; Stevenson, Abigail; Baker, Robert C.; Tang, Silin
Source:
Food microbiology 2020 v.89 pp. 103452
ISSN:
0740-0020
Subject:
genome; genome assembly,   etc   ; Salmonella; bioinformatics; computer simulation; food industry; nanopores; pipelines; prediction; serotypes;     Show all 10 Subjects
Abstract:
... The use of whole genome sequencing (WGS) data generated by short-read sequencing technologies such as the Illumina sequencing platforms has been shown to provide reliable results for Salmonella serotype prediction. Emerging long-read sequencing platforms developed by Oxford Nanopore Technologies (ONT) provide an alternative WGS method to meet the needs of industry for rapid and accurate Salmonella ...
DOI:
10.1016/j.fm.2020.103452

15. The impact of transposable elements on the structure, evolution and function of the rice genome

Author:
Akakpo, Roland; Carpentier, Marie‐Christine; Ie Hsing, Yue; Panaud, Olivier
Source:
Thenew phytologist 2020 v.226 no.1 pp. 44-49
ISSN:
0028-646X
Subject:
genome; genome-wide association study,   etc   ; Oryza sativa; chromosomes; crops; evolution; food security; genomics; rice; transposons;     Show all 10 Subjects
Abstract:
... Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently ...
DOI:
10.1111/nph.16356

16. Long walk to genomics: History and current approaches to genome sequencing and assembly

Author:
Giani, Alice Maria; Gallo, Guido Roberto; Gianfranceschi, Luca; Formenti, Giulio
Source:
Computational and Structural Biotechnology Journal 2020 v.18 pp. 9-19
ISSN:
2001-0370
Subject:
genome; genome assembly,   etc   ; DNA; analytical methods; bioinformatics; genomics; high-throughput nucleotide sequencing; nucleotide sequences;     Show all 8 Subjects
Abstract:
... Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing ...
DOI:
10.1016/j.csbj.2019.11.002
PubMed:
31890139
PubMed Central:
PMC6926122

17. Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

Author:
Gerke, Philipp; Szövényi, Péter; Neubauer, Anna; Lenz, Henning; Gutmann, Bernard; McDowell, Rose; Small, Ian; Schallenberg‐Rüdinger, Mareike; Knoop, Volker
Source:
Thenew phytologist 2020 v.225 no.5 pp. 1974-1992
ISSN:
0028-646X
Subject:
chloroplast genome; mitochondrial genome; nuclear genome,   etc   ; Arabidopsis thaliana; Physcomitrella patens; RNA editing; chloroplasts; cytidine deaminase; embryophytes; genes; mitochondria; models; proteins; synapomorphy; transcriptome;     Show all 15 Subjects
Abstract:
... Hornworts are crucial to understand the phylogeny of early land plants. The emergence of ‘reverse’ U‐to‐C RNA editing accompanying the widespread C‐to‐U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort–tracheophyte clade. C‐to‐U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcom ...
DOI:
10.1111/nph.16297

18. Microbial Chassis Development for Natural Product Biosynthesis

Author:
Xu, Xianhao; Liu, Yanfeng; Du, Guocheng; Ledesma-Amaro, Rodrigo; Liu, Long
Source:
Trends in biotechnology 2020 v.38 no.7 pp. 779-796
ISSN:
0167-7799
Subject:
genome mining,   etc   ; biochemical pathways; biosynthesis; metabolic engineering; microorganisms;     Show all 5 Subjects
Abstract:
... Engineering microbial cells to efficiently synthesize high-value-added natural products has received increasing attention in recent years. In this review, we describe the pipeline to build chassis cells for natural product production. First, we discuss recently developed genome mining strategies for identifying and designing biosynthetic modules and compare the characteristics of different host mi ...
DOI:
10.1016/j.tibtech.2020.01.002

19. Genomic and Postgenomic Diversity of Fungal Plant Biomass Degradation Approaches

Author:
de Vries, Ronald P.; Mäkelä, Miia R.
Source:
Trends in microbiology 2020 v.28 no.6 pp. 487-499
ISSN:
0966-842X
Subject:
genome,   etc   ; biotechnology; carbon cycle; fungi; genomics; phytomass; proteome; transcriptome;     Show all 8 Subjects
Abstract:
... Plant biomass degradation by fungi is a widely studied and applied field of science, due to its relevance for the global carbon cycle and many biotechnological applications. Before the genome era, many of the in-depth studies focused on a relatively small number of species, whereas now, many species can be addressed in detail, revealing the large variety in the approach used by fungi to degrade pl ...
DOI:
10.1016/j.tim.2020.01.004

20. Overcoming bottlenecks in plant gene editing

Author:
Atkins, Paul AP; Voytas, Daniel F
Source:
Current opinion in plant biology 2020 v.54 pp. 79-84
ISSN:
1369-5266
Subject:
genome,   etc   ; DNA; gene editing; nucleotide sequences; plant biology;     Show all 5 Subjects
Abstract:
... Agriculture has reached a technological inflection point. The development of novel gene editing tools and methods for their delivery to plant cells promises to increase genome malleability and transform plant biology. Whereas gene editing is capable of making a myriad of DNA sequence modifications, its widespread adoption has been hindered by a number of factors, particularly inefficiencies in cre ...
DOI:
10.1016/j.pbi.2020.01.002