Top 9 Biorxiv Papers Today in Genomics


2.019 Mikeys
#1. The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean
Daniel M Fernandes, Alissa Mittnik, Iñigo Olalde, Iosif Lazaridis, Olivia Cheronet, Nadin Rohland, Swapan Mallick, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Jens Carlsson, Brendan J Culleton, Matthew Ferry, Beatriz Gamarra, Martina Lari, Matthew Mah, Megan Michel, Alessandra Modi, Mario Novak, Jonas Oppenheimer, Kendra A Sirak, Kirstin Stewardson, Stefania Vai, Edgard Camarós, Carla Calò, Giulio Catalano, Marian Cueto, Vincenza Forgia, Marina Lozano, Elisabetta Marini, Margherita Micheletti, Roberto M Miccichè, Maria R Palombo, Damià Ramis, Vittoria Schimmenti, Pau Sureda, Luís Teira, Maria Teschler-Nicola, Douglas J Kennett, Carles Lalueza-Fox, Nick Patterson, Luca Sineo, David Caramelli, Ron Pinhasi, David Reich
A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these ancestries into the western Mediterranean where they have contributed to many populations living today remains poorly understood. We generated genome-wide ancient DNA from the Balearic Islands, Sicily, and Sardinia, increasing the number of individuals with reported data from these islands from 3 to 52. We obtained data from the oldest skeleton excavated from the Balearic islands (dating to ~2400 BCE), and show that this individual had substantial Steppe pastoralist-derived ancestry; however, later Balearic individuals had less Steppe heritage reflecting geographic heterogeneity or immigration from groups with more European first farmer-related ancestry. In Sicily, Steppe pastoralist ancestry arrived by ~2200 BCE and likely came at least in part from Spain as it was associated with...
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razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversification of various italian & sicilian languages may date to 2,000 years before roman records?
PromPreprint: The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean https://t.co/zRAc3cY8uv
BioRxivCurator: The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean https://t.co/lcFNPQr33D
reiver: RT @razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversific…
grawoig: RT @razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversific…
zenpundit: RT @razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversific…
motherlander: RT @razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversific…
theeclecticseer: RT @razibkhan: https://t.co/p1cJlVwbQs the paleo-sardinian language was probably not indo-european https://t.co/kergs38Tz2 the diversific…
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Authors: 44
Total Words: 11076
Unqiue Words: 3871

2.004 Mikeys
#2. Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
Alan Selewa, Ryan Dohn, Heather Eckart, Stephanie Lozano, Bingqing Xie, Eric Gauchat, Reem Elorbany, Katherine Rhodes, Jonathan Burnett, Yoav Gilad, Sebastian Pott, Anindita Basu
A comprehensive reference map of all cell types in the human body is necessary for improving our understanding of fundamental biological processes and in diagnosing and treating disease. High-throughput single-cell RNA sequencing techniques have emerged as powerful tools to identify and characterize cell-types in complex and heterogeneous tissues. However, extracting intact cells from tissues and organs is often technically challenging or impossible, for example in heart or brain tissue. Single-nucleus RNA sequencing provides an alternative way to obtain transcriptome profiles of such tissues. To systematically assess the differences between high-throughput single-cell and single-nuclei RNA-seq approaches, we compared Drop-seq and DroNc-seq, two microfluidic-based 3' RNA capture technologies that profile total cellular and nuclear RNA, respectively, during a time course experiment of human induced pluripotent stem cells (iPSCs) differentiating into cardiomyocytes. Clustering of time-series transcriptomes from Drop-seq and...
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A Snakemake pipeline for processing Drop-seq reads into an expression matrix

Repository: dropseq_pipeline
User: aselewa
Language: Python
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Sample Sizes : [18, 51, 22, 18, 51, 22]
Authors: 12
Total Words: 11303
Unqiue Words: 3481

2.001 Mikeys
#3. TM3'seq: a tagmentation-mediated 3' sequencing approach for improving scalability of RNA-seq experiments
Luisa F Pallares, Serge Picard, Julien F Ayroles
RNA-seq has become the standard tool for collecting genome-wide expression data in diverse fields, from quantitative genetics and medical genomics to ecology and developmental biology. However, RNA-seq library preparation is still prohibitive for many laboratories. Recently, the field of single-cell transcriptomics has reduced costs and increased throughput by adopting early barcoding and pooling of individual samples, producing a single final library containing all samples. In contrast, RNA-seq protocols where each sample is processed individually are significantly more expensive and lower throughput than single-cell approaches. Yet, many projects depend on individual library generation to preserve important samples or for follow-up re-sequencing experiments. Improving on currently available RNA-seq methods we have developed TM3'seq, a 3'-enriched library preparation protocol that uses Tn5 transposase and preserves sample identity at each step. TM3'seq is designed for high-throughput processing of individual samples (96 samples...
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razoralign: TM3'seq: a tagmentation-mediated 3' sequencing approach for improving scalability of RNA-seq experiments https://t.co/1ryY0EbIki
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Sample Sizes : [74, 3, 3, 9]
Authors: 3
Total Words: 6298
Unqiue Words: 1953

1.998 Mikeys
#4. Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility
Fernando Henrique Correr, Guilherme Kenichi Hosaka, Sergio Gregorio Perez Gomez, Mariana Cicarelli Cia, Claudia A Barros Monteiro Vitorello, Luis Eduardo Aranha Camargo, Nelson Sidnei Massola Júnior, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Puccinia kuehnii is an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak in Australia. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by the stress induced by P. kuehnii. Here we investigated changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at 0, 12, 24, 48 hours after inoculation (hai), 5 and 12 days after inoculation (dai). A de novo transcriptome was assembled with preprocessed reads, filtering out potential fungal sequences to focus on plant transcripts. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 hai and 12 dai, coinciding with the events of spore germination, haustoria post-penetration and post-sporulation. During the first 24 hours, a lack...
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Authors: 9
Total Words: 15403
Unqiue Words: 5194

1.997 Mikeys
#5. Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts
Ilias Georgakopoulos-Soares, Gene Koh, Josef Jiricny, Martin Hemberg, Serena Nik-Zainal
The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. We introduce a novel way to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our novel analytical approach reveals new insights into the contribution of DNA repair towards indel mutagenesis in human cells.
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Authors: 5
Total Words: 6873
Unqiue Words: 2051

1.997 Mikeys
#6. Mutational profiling of lipomas
Deepika Kanojia, Pushkar Dakle, Anand Mayakonda, Rajeev Parameswaran, Mark E Puhaindran, Victor Lee Kwan Min, Vikas Madan, H Phillip Koeffler
Lipomas are benign fatty tumors with a high prevalence rate, mostly found in adults but have a good prognosis. Until now, reason for lipoma occurrence not been identified. We performed whole exome sequencing to define the mutational spectrum in ten lipoma patients along with their matching control samples. We identified 412 somatic variants including missense mutations, splice site variants, frameshift indels, and stop gain/lost. Kinase genes and transcriptions factors were among the validated mutated genes critical for cell proliferation and survival. Pathway analysis revealed enrichment of calcium, Wnt and phospholipase D signaling in patients. Whole exome sequencing in lipomas identified mutations in genes with a possible role in development and progression of lipomas.
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biorxivpreprint: Mutational profiling of lipomas https://t.co/R7TlTRl0C4 #bioRxiv
biorxiv_genomic: Mutational profiling of lipomas https://t.co/Fkn5j0PEcR #biorxiv_genomic
grawoig: RT @biorxivpreprint: Mutational profiling of lipomas https://t.co/R7TlTRl0C4 #bioRxiv
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Authors: 8
Total Words: 3787
Unqiue Words: 1470

1.997 Mikeys
#7. Three-dimensional genome reorganization during mouse spermatogenesis
Zhengyu Luo, Xiaorong Wang, Ruoyu Wang, Jian Chen, Yusheng Chen, Qianlan Xu, Jun Cao, Xiaowen Gong, Ji Wu, Yungui Yang, Wenbo Li, Chunsheng Han, Fei Sun, Xiaoyuan Song
Three-dimensional genome organization plays an important role in many biological processes. Yet, how the genome is packaged at the molecular level during mammalian spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential stages during mouse spermatogenesis. We found that topological associating domains (TADs) and chromatin loops underwent highly dynamic reorganization. They displayed clear existence in primitive type A spermatogonia, disappearance at pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at TAD boundary regions (identified in primitive type A spermatogonia). Additionally, many enhancers and promoters exhibited features of open chromatin and transcription remained active at pachytene stage. A/B compartmentalization and segmentation ratio were conserved in different stages of spermatogenesis in autosomes, although there were A/B compartment switching events correlated with gene activity changes....
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Authors: 14
Total Words: 12930
Unqiue Words: 4241

1.991 Mikeys
#8. The genomic diversification of clonally propagated grapevines
Amanda Vondras, Andrea Minio, Barbara Blanco-Ulate, Rosa Figueroa, Michael Penn, Yongfeng Zhou, Danelle Seymour, Ye Zhou, Dingren Liang, Lucero Espinoza, Michael Anderson, M. Andrew Walker, Brandon Gaut, Dario Cantu
Grapevines are typically grown from cuttings rather than sexual reproduction. However, clones are not necessarily genetically identical because they accumulate somatic mutations. The purpose of this study was to better understand the consequences of clonal propagation and involved defining the nature and extent of somatic mutations throughout the genome. Sixteen Zinfandel winegrape clone genomes were sequenced and compared to one another using a highly contiguous genome reference produced from one of the clones, Zinfandel 03. Though most heterozygous variants were shared, somatic mutations accumulated in individual and subsets of clones. Overall, heterozygous mutations were most frequent in intergenic space and more frequent in introns than exons. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than genic and non-repetitive intergenic spaces, likely because of higher levels of methylation in the region and the disposition of methylated cytosines to...
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Authors: 14
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1.989 Mikeys
#9. The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations
Mosè Manni, Felipe A Simao, Hugh M Robertson, Marco A Gabaglio, Robert M Waterhouse, Bernhard Misof, Oliver Niehuis, Nikolaus Szucsich, Evgeny M Zdobnov
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod, able to regenerate lost appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. Possibly reflecting adaptation to soil life, we identified a paucity of photoreceptor genes, and by contrast the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom. Expansions of detoxification and carbohydrate metabolism gene families likely reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents a key reference for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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Authors: 9
Total Words: 0
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