Top 10 Biorxiv Papers Today in Genomics


2.035 Mikeys
#1. Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor
Can Wang, Lingbo Zhou, Xu Gao, Yanqing Ding, Bin Cheng, Guobing Zhang, Ning Cao, Yan Xu, Mingbo Shao, Liyi Zhang
Hongyingzi is a special waxy sorghum ( Sorghum bicolor L. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H), O -methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H),...
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biorxivpreprint: Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor https://t.co/Y2yM3NEZV2 #bioRxiv
biorxiv_genomic: Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor https://t.co/7PLWTPMRBO #biorxiv_genomic
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Authors: 10
Total Words: 7552
Unqiue Words: 3018

2.012 Mikeys
#2. Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells
Alexendar R Perez, Laura Sala, Richard K Perez, Joana A Vidigal
CRISPR-based high-throughput screens are a powerful method to unbiasedly assign function to a large set of genes, but current genome-wide libraries yield a substantial number of false positives and negatives. We use a retrieval-tree based approach to accurately characterize the off-target space of these libraries and show that they contain a notable fraction of highly promiscuous gRNAs. Promiscuous gRNAs are depleted from screens in a gene-independent manner, create noise in the data generated by these libraries, and ultimately lead to low accuracy in hit identification. This extensive off-targeting also contributes to low overlap between data generated by independent libraries. To minimize these problems we developed the CRISPR Specificity Correction (CSC), a computational approach that segregates on- and off-targeting effects on gRNA depletion. We demonstrate that CSC is able to reduce the occurrence of false positives, improve hit reproducibility between different libraries, and uncover both known and novel genetic dependencies...
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biorxivpreprint: Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells https://t.co/oiNjPwOzSx #bioRxiv
biorxiv_genomic: Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells https://t.co/yy76VB0NjC #biorxiv_genomic
giulianolab1: Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells https://t.co/2xdodFbknp
smuc25: RT @biorxiv_genomic: Correction of Off-Targeting in CRISPR Screens Uncovers Genetic Dependencies in Melanoma Cells https://t.co/yy76VB0NjC…
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Authors: 4
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2.008 Mikeys
#3. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability
Geoffrey Finch, Carlie Perrieta, Benjamin Davis, Sonya Nandyal, Andrew J. Rosendale, Christopher J. Holmes, Josiah D. Gantz, Drew Spacht, Samuel T. Bailey, Xiaoting Chen, Kennan Oyen, Elise M. Didion, Souvik Chakraborty, Richard E. Lee, David L. Denlinger, Stephen Matter, Geoffrey Michael Attardo, Matthew T. Weirauch, Joshua Benoit
Background: The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least two years, but adult life lasts only two weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies are used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. Results: RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other...
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biorxivpreprint: Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability https://t.co/J3ELgSsCsQ #bioRxiv
biorxiv_genomic: Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by ... https://t.co/vdhqHZ6qWV #biorxiv_genomic
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Authors: 19
Total Words: 19453
Unqiue Words: 4833

2.001 Mikeys
#4. High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome
Annarita Marrano, Monica Britton, Paulo Adriano Zaini, Aleksey Zimin, Rachael Workman, Daniela Puiu, Luca Bianco, Erica Adele Di Pierro, Brian Allen, Sandeep Chakraborty, Michela Troggio, Charles Leslie, Winston Timp, Abhaya Dendekar, Steven Salzberg, David B. Neale
The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic and proteomic information for a full determinism of walnut biological processes. Here we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0), obtained combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features a 84.4-fold increase in N50 size, and the 16 chromosomal pseudomolecules fully-assembled, nine of which presenting telomere sequences at both ends. Using full-length transcripts from single-molecule real-time sequencing, we predicted 40,491 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) are full-length, which represents a great improvement compared to...
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solgenetics: High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome https://t.co/H5QrMbObWF
ChengChiangWu: RT @biorxiv_genomic: High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome https://t.co/OHz5YI2PvB #bior…
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Authors: 16
Total Words: 0
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1.999 Mikeys
#5. Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes
Axel Thiefry, Jette Bornholdt, Maxim Ivanov, Peter Brodersen, Albin Sandelin
In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Similarly, active enhancer regions in animals initiate transcription of exosome-sensitive enhancer RNAs (eRNAs). Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs. Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs and eRNAs in A. thaliana. While PROMPTs are overall rare in A. thaliana, about 100 clear cases of exosome-sensitive PROMPTs and 113 loci producing eRNA-like transcripts were identified. In addition, we found ~200 transcription start sites within 3'-UTR-encoding regions that produce unspliced exosome-sensitive antisense RNAs covering much of the cognate pre-mRNA. A typical representative of this class of...
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giulianolab1: Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes https://t.co/bPCVjd9XHJ
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1.998 Mikeys
#6. Dynamic Transcriptome, Accessible Genome and PGR Cistrome Profiles in the Human Myometrium
San-Pin Wu, Matthew L Anderson, Tianyuan Wang, Lecong Zhou, Olivia M Emery, Xilong Li, Francesco John DeMayo
The myometrium undergoes structural and functional remodeling during pregnancy. We hypothesize that myometrial genomic elements alter correspondingly in preparation for parturition. Human myometrial tissues from nonpregnant (NP) and term pregnant (TP) human subjects were examined by RNAseq, ATAC-seq and PGR ChIP-seq assays to profile transcriptome, assessible genome and PGR occupancy. NP and TP specimens exhibit 2890 differentially expressed genes, reflecting an increase of metabolic, inflammatory and PDGF signaling, among others, in adaptation to pregnancy. At the epigenome level, patterns of accessible genome change between NP and TP myometrium, leading to altered enrichment of binding motifs for hormone and muscle regulators such as the progesterone receptor (PGR), Kruppel-like factors and MEF2A transcription factors. PGR genome occupancy exhibits a significant difference between the two stages of the myometrium, concomitant with distinct transcriptomic profiles including genes such as ENO1, LHDA, and PLCL1 in the glycolytic...
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Authors: 7
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1.998 Mikeys
#7. Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects
Nathan E Hall, Jared Mamrot, Christopher M.A. Frampton, Prue Read, Edward J Steele, Robert J Bischof, Robyn A Lindley
Background: Deaminases play an important role in shaping inherited and somatic variants. Disease related SNVs are associated with deaminase mutagenesis and genome instability. Here, we investigate the reproducibility and variance of whole exome SNV calls in blood and saliva of healthy subjects and analyze variants associated with AID, ADAR, APOBEC3G and APOBEC3B deaminase sequence motifs. Methods: Samples from twenty-four healthy Caucasian volunteers, allocated into two groups, underwent whole exome sequencing. Group 1 (n=12) analysis involved one blood and four saliva replicates. A single saliva sample was sequenced for Group 2 subjects (n=12). Overall, a total of 72 whole exome datasets were analyzed. Biological (Group 1 & 2) and technical (Group 1) variance of SNV calls and deaminase metrics were calculated and analyzed using intraclass correlation coefficients. Candidate somatic SNVs were identified and evaluated. Results: We report high blood-saliva concordance in germline SNVs from whole exome sequencing. Concordant SNVs,...
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biorxivpreprint: Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects https://t.co/jj5bwAVYjK #bioRxiv
biorxiv_genomic: Deaminase associated single nucleotide variants in blood and saliva-derived exomes from healthy subjects https://t.co/qwAX0oiVus #biorxiv_genomic
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1.998 Mikeys
#8. Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot
Tania Valdivia-Carrillo, Axayacatl Rocha-Olivares, Hector Reyes-Bonilla, Jose Francisco Dominguez-Contreras, Adrian Munguia-Vega
Significant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly...
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Authors: 5
Total Words: 10631
Unqiue Words: 3591

1.997 Mikeys
#9. The BSGatlas: An enhanced annotation of genes and transcripts for the Bacillus subtilis genome with improved information access
Adrian Sven Geissler, Christian Anthon, Enrique González-Tortuero, Line Dahl Poulsen, Thomas Beuchert Kallehauge, Stefan Ernst Seemann, Jeppe Vinther, Jan Gorodkin
The genome of Bacillus subtilis continues to provide exiting genomic insights. However, the growing collective genomic knowledge about this micro-organism is spread across multiple annotation resources. Thus, the full annotation is not directly accessible neither for specific genes nor for large-scale high-throughput analyses. Furthermore, access to annotation of non-coding RNA genes (ncRNAs) and polycistronic mRNAs is difficult. To address these challenges we introduce the Bacillus subtilis genome atlas, BSGatlas, in which we integrate and unify multiple existing annotation resources. Our integration provides twice as many ncRNAs than the individual resources, improves the positional annotation for 70% of the combined ncRNAs, and makes it possible to infer specific ncRNA types. Moreover, we unify known transcription start sites, termination, and transcriptional units (TUs) as a comprehensive transcript map. This transcript map implies 815 new TUs and 6,164 untranslated regions (UTRs), which is a five-fold increase over existing...
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1.997 Mikeys
#10. Reference transcriptome data in silkworm, Bombyx mori
Kakeru Yokoi, Takuya Tsubota, Sun Jianqiang, Akiya Joraku, Hideki Sezutsu, Hidemasa Bono
The silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we constructed a reference transcriptome data set using the reference genome data and RNA-seq data of 10 tissues from P50T strain larvae. Reference transcriptome data contained 51,926 transcripts, with 39,619 having one or more coding sequence region. The abundance of each transcript in the 10 tissues as well as 5 tissues from other strain larvae was estimated, and hierarchical clustering was performed. The results obtained showed that data on abundance were highly reproducible and there here is a little difference of transcriptome abundance between the two strain larvae. New isoforms of silk-related genes were searched for in the reference transcriptomes, and the longest isoform of sericin-1 possessing a long exon was identified. We also extracted transcripts that were strongly expressed in one...
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biorxivpreprint: Reference transcriptome data in silkworm, Bombyx mori https://t.co/uAKObsNVdt #bioRxiv
biorxiv_genomic: Reference transcriptome data in silkworm, Bombyx mori https://t.co/iMfmdAHbiz #biorxiv_genomic
bonohu: RT @biorxiv_genomic: Reference transcriptome data in silkworm, Bombyx mori https://t.co/iMfmdAHbiz #biorxiv_genomic
mtanichthys: RT @biorxivpreprint: Reference transcriptome data in silkworm, Bombyx mori https://t.co/uAKObsNVdt #bioRxiv
EvoEpi: RT @biorxivpreprint: Reference transcriptome data in silkworm, Bombyx mori https://t.co/uAKObsNVdt #bioRxiv
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Authors: 6
Total Words: 7149
Unqiue Words: 2401

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