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1. Targeting Ascomycota genomes: what and how big?

Author:
Hill, Rowena; Leitch, Ilia J.; Gaya, Ester
Source:
Fungal biology reviews 2021 v.36 pp. 52-59
ISSN:
1749-4613
Subject:
genome; genome assembly,   etc   ; Ascomycota; fungi; genomics; mycology;     Show all 6 Subjects
Abstract:
... Gap analysis of the available genomic data (i.e. identifying taxonomic groups with no representative genome assemblies) is a fundamental first step to design effective sampling strategies for whole genome sequencing (WGS) initiatives. We identified the significant holes that remain in genomic resources of the Ascomycota – the largest fungal phylum including many species of medicinal, ecological an ...
DOI:
10.1016/j.fbr.2021.03.003

2. A generalization of t-SNE and UMAP to single-cell multimodal omics

Author:
Do, Van Hoan; Canzar, Stefan
Source:
Genome biology 2021 v.22 no.1 pp. 130
ISSN:
1474-760X
Subject:
genome,   etc   ; RNA; data collection;     Show all 3 Subjects
Abstract:
... Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP. We introduce j-SNE and j-UMAP as their natural generalizations to the joint visualization of multimodal omics data. Our approach automatically ...
DOI:
10.1186/s13059-021-02356-5

3. MARS: leveraging allelic heterogeneity to increase power of association testing

Author:
Hormozdiari, Farhad; Jung, Junghyun; Eskin, Eleazar; J. Joo, Jong Wha
Source:
Genome biology 2021 v.22 no.1 pp. 128
ISSN:
1474-760X
Subject:
genome,   etc   ; phenotype; risk;     Show all 3 Subjects
Abstract:
... In standard genome-wide association studies (GWAS), the standard association test is underpowered to detect associations between loci with multiple causal variants with small effect sizes. We propose a statistical method, Model-based Association test Reflecting causal Status (MARS), that finds associations between variants in risk loci and a phenotype, considering the causal status of variants, on ...
DOI:
10.1186/s13059-021-02353-8

4. Samplot: a platform for structural variant visual validation and automated filtering

Author:
Belyeu, Jonathan R.; Chowdhury, Murad; Brown, Joseph; Pedersen, Brent S.; Cormier, Michael J.; Quinlan, Aaron R.; Layer, Ryan M.
Source:
Genome biology 2021 v.22 no.1 pp. 161
ISSN:
1474-760X
Subject:
genome,   etc   ; automation; humans; prioritization;     Show all 4 Subjects
Abstract:
... Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence alignments necessary to adjudicate purported SVs across samples and sequencing technologies. These images can be rapidly reviewed to curate large SV call sets. Samplot is applicable to many biol ...
DOI:
10.1186/s13059-021-02380-5

5. scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing

Author:
Wilson, Gavin W.; Derouet, Mathieu; Darling, Gail E.; Yeung, Jonathan C.
Source:
Genome biology 2021 v.22 no.1 pp. 144
ISSN:
1474-760X
Subject:
genome,   etc   ; RNA; sequence analysis;     Show all 3 Subjects
Abstract:
... Identifying single nucleotide variants has become common practice for droplet-based single-cell RNA-seq experiments; however, presently, a pipeline does not exist to maximize variant calling accuracy. Furthermore, molecular duplicates generated in these experiments have not been utilized to optimally detect variant co-expression. Herein, we introduce scSNV designed from the ground up to “collapse” ...
DOI:
10.1186/s13059-021-02364-5

6. In the Era of the Actionable Genome, Everyone is Responsible

Author:
Houtman, Diewertje; Vijlbrief, Boy; Riedijk, Sam R.
Source:
Trends in biotechnology 2021 v.39 no.7 pp. 641-643
ISSN:
0167-7799
Subject:
genome,   etc   ; biotechnology; genomics; society;     Show all 4 Subjects
Abstract:
... Genomics professionals and the general public have a responsibility to bridge the gap between science and society. The general public has a responsibility to deliberate, as their choices not only impact themselves but also shape society. Conversely, genomics professionals have a responsibility to enable the process of opinion formation. ...
DOI:
10.1016/j.tibtech.2020.11.009

7. Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules

Author:
Singh, Rajveer; Chandel, Shivani; Ghosh, Arijit; Dey, Dhritiman; Chakravarti, Rudra; Roy, Syamal; Ravichandiran, V.; Ghosh, Dipanjan
Source:
Molecular biotechnology 2021 v.63 no.6 pp. 459-476
ISSN:
1073-6085
Subject:
genome,   etc   ; biotechnology; yeasts;     Show all 3 Subjects
Abstract:
... Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas protein technology area is rapidly growing technique for genome editing and modulation of transcription of several microbes. Successful engineering in microbes requires an emphasis on the aspect of efficiency and targeted aiming, which can be employed using CRISPR/Cas system. Hence, this type of system is u ...
DOI:
10.1007/s12033-021-00310-1

8. Rice bioinformatics in the genomic era: Status and perspectives

Author:
Jia, Lei; Xie, Lingjuan; Lao, Sangting; Zhu, Qian-Hao; Fan, Longjiang
Source:
The crop journal 2021 v.9 no.3 pp. 609-621
ISSN:
2214-5141
Subject:
genome,   etc   ; bioinformatics; genomics; rice;     Show all 4 Subjects
Abstract:
... Rice is one of cereal crops and a model species for monocots. Since the release of the first draft rice genome sequences in 2002, considerable progress has been achieved in rice genomic researches, thanks to rapid development and efficient utilization of bioinformatics methods and tools. In this review, we summarize the progress of studies of rice genome sequencing and other omics and introduce th ...
DOI:
10.1016/j.cj.2021.03.003

9. The Evolution of Concepts about the Biological Role of Lampbrush Chromosomes

Author:
Saifitdinova, A. F.; Galkina, S. A.; Gaginskaya, E. R.
Source:
Russian journal of genetics 2021 v.57 no.5 pp. 499-514
ISSN:
1022-7954
Subject:
genome,   etc   ; genomics; mitosis; models;     Show all 4 Subjects
Abstract:
... The review is focused on the development of ideas about the role of one of the most mysterious phenomena of developmental biology, i.e., the transformation of chromosomes into the so-called lampbrush chromosomes (LBCs). Eukaryotic chromosomes in the LBC phase are characterized by a low level of condensation and discrete structure formed by numerous linearly arranged compact chromomeres, from which ...
DOI:
10.1134/S1022795421050100

10. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases

Author:
Rius, Rocio; Compton, Alison G.; Baker, Naomi L.; Welch, AnneMarie E.; Coman, David; Kava, Maina P.; Minoche, Andre E.; Cowley, Mark J.; Thorburn, David R.; Christodoulou, John
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
nuclear genome,   etc   ; blood; mitochondria;     Show all 3 Subjects
Abstract:
... Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related c ...
DOI:
10.3390/genes12040607

11. Detection of genome‐edited and endogenously expressed G protein‐coupled receptors

Author:
Soave, Mark; Stoddart, Leigh A.; White, Carl W.; Kilpatrick, Laura E.; Goulding, Joëlle; Briddon, Stephen J.; Hill, Stephen J.
Source:
TheFEBS journal 2021 v.288 no.8 pp. 2585-2601
ISSN:
1742-464X
Subject:
genome,   etc   ; drugs; fluorescence; ligands;     Show all 4 Subjects
Abstract:
... G protein‐coupled receptors (GPCRs) are the largest family of membrane receptors and major targets for FDA‐approved drugs. The ability to quantify GPCR expression and ligand binding characteristics in different cell types and tissues is therefore important for drug discovery. The advent of genome editing along with developments in fluorescent ligand design offers exciting new possibilities to prob ...
DOI:
10.1111/febs.15729

12. See(quence) and ye shall find: higher-order genome folding in intact single cells

Author:
Pham, Kenneth; Nikish, Alexandria; Phillips-Cremins, Jennifer E.
Source:
Molecular cell 2021 v.81 no.6 pp. 1130-1132
ISSN:
1097-2765
Subject:
genome,   etc   ; ; fibroblasts; humans; mice;     Show all 5 Subjects
Abstract:
... Payne et al. (2020) combine in situ imaging and ex situ sequencing via spatially resolved unique molecular barcodes to query higher-order genome folding patterns in intact single nuclei from mouse embryos and human fibroblasts. ...
DOI:
10.1016/j.molcel.2021.02.035

13. No pains, no gains: how chromosome fragmentation promotes gene amplification

Author:
Zhang, Cheng-Zhong
Source:
Molecular cell 2021 v.81 no.5 pp. 901-904
ISSN:
1097-2765
Subject:
genome,   etc   ; chromosomes; gene amplification;     Show all 3 Subjects
Abstract:
... Combining live-cell imaging, cytogenetics, genome sequencing, and in vitro evolution, Shoshani et al. (2020) revealed deep connections between chromothripsis, the catastrophic shattering of a chromosome in abnormal nuclear structures, and gene amplification, a frequent culprit of oncogenic activation. ...
DOI:
10.1016/j.molcel.2021.02.018

14. Pan-RNA editing analysis of the bovine genome

Author:
Cai, Wentao; Shi, Lijun; Cao, Mingyue; Shen, Dan; Li, Junya; Zhang, Shengli; Song, Jiuzhou
Source:
RNA biology 2021 v.18 no.3 pp. 368-381
ISSN:
1555-8584
Subject:
genome,   etc   ; cattle; nucleotides;     Show all 3 Subjects
Abstract:
... RNA editing is an essential process for modifying nucleotides at specific RNA sites during post-transcription in many species. However, its genomic landscape and characters have not been systematically explored in the bovine genome. In the present study, we characterized global RNA editing profiles from 50 samples of cattle and revealed a range of RNA editing profiles in different tissues. Most ed ...
DOI:
10.1080/15476286.2020.1807724

15. Step by Step about Germ Cells Development in Canine

Author:
de Souza, Aline Fernanda; Pieri, Naira Caroline Godoy; Martins, Daniele dos Santos
Source:
Animals 2021 v.11 no.3
ISSN:
2076-2615
Subject:
genome,   etc   ; ; dogs; models; therapeutics;     Show all 5 Subjects
Abstract:
... Primordial germ cells (PGCs) have been described as precursors of gametes and provide a connection within generations, passing on the genome to the next generation. Failures in the formation of gametes/germ cells can compromise the maintenance and conservation of species. Most of the studies with PGCs have been carried out in mice, but this species is not always the best study model when transposi ...
DOI:
10.3390/ani11030598

16. User-centric genomics infrastructure: trends and technologies

Author:
Krishna, Ritesh; Elisseev, Vadim
Source:
Genome 2021 v.64 no.4 pp. 467-475
ISSN:
1480-3321
Subject:
genome,   etc   ; genomics; infrastructure; landscapes;     Show all 4 Subjects
Abstract:
... Genomics is both a data- and compute-intensive discipline. The success of genomics depends on an adequate informatics infrastructure that can address growing data demands and enable a diverse range of resource-intensive computational activities. Designing a suitable infrastructure is a challenging task, and its success largely depends on its adoption by users. In this article, we take a user-centr ...
DOI:
10.1139/gen-2020-0096

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

Author:
Rhie, Arang; Walenz, Brian P.; Koren, Sergey; Phillippy, Adam M.
Source:
Genome biology 2020 v.21 no.1 pp. 245
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; humans;     Show all 3 Subject
Abstract:
... Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. ...
DOI:
10.1186/s13059-020-02134-9

18. AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data

Author:
Fletcher, Kyle; Zhang, Lin; Gil, Juliana; Han, Rongkui; Cavanaugh, Keri; Michelmore, Richard
Source:
Genome biology 2021 v.22 no.1 pp. 115
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; Bremia lactucae; chromosome mapping; genotype;     Show all 5 Subjects
Abstract:
... Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole ge ...
DOI:
10.1186/s13059-021-02326-x

19. Genome Resources for Seven Fungal Isolates That Cause Dollar Spot Disease in Turfgrass, Including Clarireedia jacksonii and C. monteithiana

Author:
Crouch, Jo Anne; Beirn, Lisa A.; Boehm, Michael J.; Carbone, Ignazio; Clarke, Bruce B.; Kerns, James P.; Malapi-Wight, Martha; Mitchell, Thomas K.; Venu, R. C.; Tredway, Lane P.
Source:
Plant disease 2021 v.105 no.3 pp. 691-694
ISSN:
0191-2917
Subject:
genome; genome assembly,   etc   ; disease control; fungi; pathogens; turf grasses;     Show all 6 Subjects
Abstract:
... Fungi in the genus Clarireedia are widespread and destructive pathogens of grasses worldwide, and are best known as the causal agents of dollar spot disease in turfgrass. Here, we report genome assemblies of seven Clarireedia isolates, including ex-types of the two most widespread species, Clarireedia jacksonii and C. monteithiana. These datasets provide a valuable resource for ongoing studies of ...
Handle:
10113/7071278
DOI:
10.1094/PDIS-06-20-1296-A

20. Performance comparison of four types of target enrichment baits for exome DNA sequencing

Author:
Zhou, Juan; Zhang, Mancang; Li, Xiaoqi; Wang, Zhuo; Pan, Dun; Shi, Yongyong
Source:
Hereditas 2021 v.158 no.1 pp. 10
ISSN:
1601-5223
Subject:
genome,   etc   ; RNA; single-stranded DNA;     Show all 3 Subjects
Abstract:
... BACKGROUND: Next-generation sequencing technology is developing rapidly and target capture sequencing has become an important technique. Several different platforms for library preparation and target capture with different bait types respectively are commercially available. Here we compare the performance of the four platforms with different bait types to find out their advantages and limitations. ...
DOI:
10.1186/s41065-021-00171-3