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1. The Strawberry Tales: Size Matters

Author:
Vergauwen, David; De Smet, Ive
Source:
Trends in plant science 2019 v.24 no.1 pp. 1-3
ISSN:
1360-1385
Subject:
genome,   etc   ; domestication; odors; strawberries;     Show all 4 Subjects
Abstract:
... The history of the strawberry is one of ambitious kings and cunning spies, overseas adventures, and religious symbolism. Here, we will tell these stories, illustrated by relevant paintings and drawings, to give insight into the domestication of the strawberry. Furthermore, we will briefly discuss the complex strawberry genomes and aroma. ...
DOI:
10.1016/j.tplants.2018.10.007

2. A genome-wide view of mutations in respiration-deficient mutants of Saccharomyces cerevisiae selected following carbon ion beam irradiation

Author:
Guo, Xiaopeng; Zhang, Miaomiao; Gao, Yue; Cao, Guozhen; Yang, Yang; Lu, Dong; Li, Wenjian
Source:
Applied microbiology and biotechnology 2019 v.103 no.4 pp. 1851-1864
ISSN:
0175-7598
Subject:
mitochondrial genome; nuclear genome,   etc   ; Saccharomyces cerevisiae; breeding; carbon; chromosomes; genes; irradiation; mitochondria; mutants; screening; spontaneous mutation;     Show all 12 Subjects
Abstract:
... Mitochondrial dysfunction in Saccharomyces cerevisiae was selected as a marker of ion penetration following carbon ion beam (CIB) irradiation. Respiration-deficient mutants were screened. Following confirmation of negligible spontaneous mutation, eight genetically stable S. cerevisiae respiration-deficient mutant strains and a control strain were resequenced with ~ 200-fold read depth. Strategies ...
DOI:
10.1007/s00253-019-09626-0

3. Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics

Author:
Rogers, Jeffrey
Source:
Genome biology 2018 v.19 no.1 pp. 115
ISSN:
1474-760X
Subject:
genome,   etc   ; evolution; genomics;     Show all 3 Subjects
Abstract:
... The main goal and promise of comparative genomics has been to create a comprehensive catalog of genomic information and function across the phenomenal diversity of living systems. A recent study has demonstrated the evolutionary insights possible by generating high-quality whole-genome assemblies from multiple species of a clade. ...
DOI:
10.1186/s13059-018-1500-7

4. GIVE: portable genome browsers for personal websites

Author:
Cao, Xiaoyi; Yan, Zhangming; Wu, Qiuyang; Zheng, Alvin; Zhong, Sheng
Source:
Genome biology 2018 v.19 no.1 pp. 92
ISSN:
1474-760X
Subject:
genome,   etc   ; Internet; genomics;     Show all 3 Subjects
Abstract:
... Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome ...
DOI:
10.1186/s13059-018-1465-6

5. 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

Author:
Kim, Ji Hun; Titus, Katelyn R.; Gong, Wanfeng; Beagan, Jonathan A.; Cao, Zhendong; Phillips-Cremins, Jennifer E.
Source:
Methods 2018 v.142 pp. 39-46
ISSN:
1046-2023
Subject:
genome,   etc   ; chromatin; mammals; topology;     Show all 4 Subjects
Abstract:
... Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput co ...
DOI:
10.1016/j.ymeth.2018.05.005

6. SnapShot: TCGA-Analyzed Tumors

Author:
Blum, Amy; Wang, Peggy; Zenklusen, Jean C.
Source:
Cell 2018 v.173 pp. 530
ISSN:
0092-8674
Subject:
genome,   etc   ; classification; neoplasms;     Show all 3 Subjects
Abstract:
... This SnapShot provides a list of the tumor types characterized by The Cancer Genome Atlas (TCGA) program. Key findings shown are the most relevant discoveries described in each marker paper for the tumor type. ...
DOI:
10.1016/j.cell.2018.03.059

7. Correction to: Genome characterization and distribution of Taro bacilliform CH virus on taro in Hawaii, USA

Author:
Wang, Yanan; Borth, WayneB.; Green, JamesC.; Hamim, Islam; Cao, Keqiang; Hu, JohnS.; Melzer, MichaelJ.
Source:
European journal of plant pathology 2018 v.150 no.2 pp. 547
ISSN:
0929-1873
Subject:
genome,   etc   ; taro; viruses; Hawaii;     Show all 4 Subjects
Abstract:
... Due to some error captions for Fig. 1 and Fig. 2 have somehow been switched and needs to be read as: Fig. 1: Genome organization of Taro bacilliform CH virus (TaBCHV) Hawaii Srain. ...
DOI:
10.1007/s10658-017-1391-6

8. Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Author:
Liu, Jiabin; Yu, Jiaojiao; Zhou, Ming; Yang, Jiandong
Source:
International journal of biological macromolecules 2019 v.125 pp. 423-431
ISSN:
0141-8130
Subject:
mitochondrial genome,   etc   ; Agamidae; gene rearrangement; lizards; mitochondrial genes; phylogeny; China;     Show all 7 Subjects
Abstract:
... Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae ...
DOI:
10.1016/j.ijbiomac.2018.12.068

9. TGACG‐BINDING FACTORs (TGAs) and TGA‐interacting CC‐type glutaredoxins modulate hyponastic growth in Arabidopsis thaliana

Author:
Li, Ning; Muthreich, Martin; Huang, Li‐Jun; Thurow, Corinna; Sun, Tongjun; Zhang, Yuelin; Gatz, Christiane
Source:
Thenew phytologist 2019 v.221 no.4 pp. 1906-1918
ISSN:
0028-646X
Subject:
genome,   etc   ; Arabidopsis thaliana; hyponasty; mutants; protein-protein interactions; proteins;     Show all 6 Subjects
Abstract:
... TGACG‐BINDING FACTORs (TGAs) control the developmental or defense‐related processes. In Arabidopsis thaliana, the functions of at least TGA2 and PERIANTHIA (PAN) can be repressed by interacting with CC‐type glutaredoxins, which have the potential to control the redox state of target proteins. As TGA1 can be redox modulated in planta, we analyzed whether some of the 21 CC‐type glutaredoxins (ROXYs) ...
DOI:
10.1111/nph.15496

10. Mitochondrial genome of Paruterina candelabraria (Cestoda: Paruterinidae), with implications for the relationships between the genera Cladotaenia and Paruterina

Author:
Guo, Aijiang; Wang, Li; Zhang, Shaohua; Zheng, Yadong; Georgiev, Boyko B.; Luo, Xuenong; Huang, Siyang; Cai, Xuepeng
Source:
Acta tropica 2019 v.189 pp. 1-5
ISSN:
0001-706X
Subject:
mitochondrial genome,   etc   ; Bayesian theory; Taeniidae; genes; mitochondria; nucleotide sequences; phylogeny;     Show all 7 Subjects
Abstract:
... The taxonomic concept for the family Paruterinidae is controversial, especially concerning the position of the genus Cladotaenia, since the latter genus has been placed sometimes in other families, i.e. in the Taeniidae or in the distinct family Cladotaeniidae; finding a solution based on morphological data is difficult and molecular data on paruterinids and related groups are scarce. In this stud ...
DOI:
10.1016/j.actatropica.2018.09.016

11. On the mechanisms of development in monocot and eudicot leaves

Author:
Conklin, Phillip A.; Strable, Josh; Li, Shujie; Scanlon, Michael J.
Source:
Thenew phytologist 2019 v.221 no.2 pp. 706-724
ISSN:
0028-646X
Subject:
genome,   etc   ; Arabidopsis; Liliopsida; grasses; leaf development; leaves; models; ontogeny; tissues;     Show all 9 Subjects
Abstract:
... Contents Summary 706 I. Introduction 707 II. Leaf zones in monocot and eudicot leaves 707 III. Monocot and eudicot leaf initiation: differences in degree and timing, but not kind 710 IV. Reticulate and parallel venation: extending the model? 711 V. Flat laminar growth: patterning and coordination of adaxial–abaxial and mediolateral axes 713 VI. Stipules and ligules: ontogeny of primordial elaborat ...
DOI:
10.1111/nph.15371

12. Strategies for the Enrichment and Selection of Genetically Modified Cells

Author:
Ren, Chonghua; Xu, Kun; Segal, David Jay; Zhang, Zhiying
Source:
Trends in biotechnology 2019 v.37 no.1 pp. 56-71
ISSN:
0167-7799
Subject:
genome,   etc   ; gene editing; gene therapy; genomics; loci; nucleases; screening;     Show all 7 Subjects
Abstract:
... Programmable artificial nucleases have transitioned over the past decade from ZFNs and TALENs to CRISPR/Cas systems, which have been ubiquitously used with great success to modify genomes. The efficiencies of knockout and knockin vary widely among distinct cell types and genomic loci and depend on the nuclease delivery and cleavage efficiencies. Moreover, genetically modified cells are almost phen ...
DOI:
10.1016/j.tibtech.2018.07.017

13. The importance of designating type material for uncultured taxa

Author:
Chuvochina, Maria; Rinke, Christian; Parks, Donovan H.; Rappé, Michael S.; Tyson, Gene W.; Yilmaz, Pelin; Whitman, William B.; Hugenholtz, Philip
Source:
Systematic and applied microbiology 2019 v.42 no.1 pp. 15-21
ISSN:
0723-2020
Subject:
genome,   etc   ; Archaea; bacteria; biological nomenclature; nucleotide sequences; prokaryotic cells;     Show all 6 Subjects
Abstract:
... Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank o ...
DOI:
10.1016/j.syapm.2018.07.003

14. A comparative evaluation of genome assembly reconciliation tools

Author:
Alhakami, Hind; Mirebrahim, Hamid; Lonardi, Stefano
Source:
Genome biology 2017 v.18 no.1 pp. 93
ISSN:
1474-760X
Subject:
genome; genome assembly,   etc   ; data collection;     Show all 3 Subject
Abstract:
... BACKGROUND: The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select t ...
DOI:
10.1186/s13059-017-1213-3

15. Three invariant Hi-C interaction patterns: Applications to genome assembly

Author:
Oddes, Sivan; Zelig, Aviv; Kaplan, Noam
Source:
Methods 2018 v.142 pp. 89-99
ISSN:
1046-2023
Subject:
genome; genome assembly,   etc   ; genomics; high-throughput nucleotide sequencing; industry; loci;     Show all 6 Subjects
Abstract:
... Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the ...
DOI:
10.1016/j.ymeth.2018.04.013

16. The challenges of integrating two genomes in one cell

Author:
Hagström, Erik; Andersson, Siv GE
Source:
Current opinion in microbiology 2018 v.41 pp. 89-94
ISSN:
1369-5274
Subject:
mitochondrial genome; nuclear genome,   etc   ; bacteria; genes; information processing; mitochondria;     Show all 6 Subjects
Abstract:
... Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single ...
DOI:
10.1016/j.mib.2017.12.003

17. Correction to: Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line

Author:
Wheeler, Nicolas J.; Dinguirard, Nathalie; Marquez, Joshua; Gonzalez, Adrian; Zamanian, Mostafa; Yoshino, Timothy P.; Castillo, Maria G.
Source:
Parasites & vectors 2018 v.11 no.1 pp. 566
ISSN:
1756-3305
Subject:
genome,   etc   ; Biomphalaria glabrata; cell lines;     Show all 3 Subjects
Abstract:
... Following publication of the original article [], the authors reported an error in figure 1: ...
DOI:
10.1186/s13071-018-3135-7

18. Investigating enhancer evolution with massively parallel reporter assays

Author:
Kwon, Soo Bin; Ernst, Jason
Source:
Genome biology 2018 v.19 no.1 pp. 114
ISSN:
1474-760X
Subject:
genome,   etc   ; enhancer elements; evolution; liver;     Show all 4 Subjects
Abstract:
... A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...
DOI:
10.1186/s13059-018-1502-5

19. Recent advances in plant and animal genomics are taking agriculture to new heights

Author:
Beiki, Hamid; Eveland, Andrea L.; Tuggle, Christopher K.
Source:
Genome biology 2018 v.19 no.1 pp. 48
ISSN:
1474-760X
Subject:
genome,   etc   ; animals; genomics; United States;     Show all 4 Subjects
Abstract:
... A report on the International Plant and Animal Genomes (PAG) conference held in San Diego, USA, 13–17 January 2018. ...
DOI:
10.1186/s13059-018-1427-z

20. DiscoVista: Interpretable visualizations of gene tree discordance

Author:
Sayyari, Erfan; Whitfield, James B.; Mirarab, Siavash
Source:
Molecular phylogenetics and evolution 2018 v.122 pp. 110-115
ISSN:
1055-7903
Subject:
genome,   etc   ; Internet; computer software; phylogeny;     Show all 4 Subjects
Abstract:
... Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences. Interpretive ways of measuring and visualizing discordance are needed, both among al ...
DOI:
10.1016/j.ympev.2018.01.019