上个月和预印本有关的最大新闻非nature的黄金开放获取（golden open access）莫属了【1】。该协议规定：如果作者希望以完全开放获取形式发表文章，则需要支付11390美元（9500欧元）的开放获取费（非强制）。开放获取大潮来势汹汹。关于开放获取和其不同形式，我们曾在此前有过一篇推送介绍【2】，这里只简单说一下：科学出版是需要烧钱的，出版商又要赚钱，所以他们要想方设法拿到这笔钱。传统上这笔钱由读者支付（一般是学校或科研机构的图书馆订购但只有订购单位能看文章），而现今另一种流行方式就是由作者支付，所谓开放获取（换言之作者出钱让任何人都可以看自己的文章）。
10月初，德国著名科研机构马克思普朗克研究所（max plank institute）刚刚同Springer Nature出版集团达成协议，“该协议允许参与机构的作者在 Nature 及其 33 种系列期刊上免费发表开放获取（OA）文章，参与机构还可以获得对 Nature 系列期刊的阅读权限，包括 Nature Review 系列期刊和所有即将推出的 Nature 品牌刊“【1】。该协议将于21年1月生效，为期四年。对此，曾接受过我们生信人专访的新兴论文发表（准确地说是预印本文章推荐）平台PCI（https://peercommunityin.org/）也发推，内容很简单：
在此，小编向大家建议，试试biorxiv + PCI吧！这里有完全免费的平台（biorixv），以及高水平科学家的审稿被接受后即可获得doi和引用，日益增长的认可度，理论上可取得与常规高水平杂志上发表文章类似的效果，且此后还可以继续向其他杂志投稿（PCI）【3】。
每月月底，小编都会有些头疼，因为在每月大量的biorxiv预印本中选出小编眼中十篇所谓的“生信好文”实在不是一件容易的事，且疏漏难免。从本期开始，我们会通过“查缺补漏”的方式为大家呈递这些在当月被忽略的文章。第一篇“补漏”的文章，来自巴黎萨克雷大学（Université Paris-Saclay）的研究团队领导的一项研究，科学家们对Tara Oceans项目中的宏基因组数据进行分析，完成了其中700个真核生物微生物组的分箱，可以说极大扩充了我们对于海洋原生生物的认识。与此同时，我们也在副推中为大家带来这一全球著名的大洋科考项目的更多介绍。
Nucleotide-resolution bacterial pan-genomics with reference graphs
Bacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core) - the alignable fraction of two genomes from a single species might be only 50%. Standard tools therefore analyse mutations only in the core genome, ignoring accessory mutations. We present a novel pan-genome graph structure and algorithms implemented in the software pandora, which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show, for rare variants, pandora recovers at least 13k more SNPs than single-reference based tools, achieving equal or better error rates with Nanopore as with Illumina data, and providing a stable framework for analysing diverse samples without reference bias. This is a significant step towards comprehensive analyses of bacterial genetic variation.
2.【枢纽】斯坦福大学Howard Chang：染色体外DNA 枢纽（EcDNA hubs）对原癌基因表达的重要作用
EcDNA hubs drive cooperative intermolecular oncogene expression
Extrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation1. Gene expression typically involves distal enhancer DNA elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs, comprised of ~10-100 ecDNAs clustered in the nucleus of interphase cells, drive intermolecular enhancer input for amplified oncogene expression. Single-molecule sequencing, single-cell multiome, and 3D enhancer connectome reveal subspecies of MYC-PVT1 ecDNAs lacking enhancers that access intermolecular and ectopic enhancer-promoter interactions in ecDNA hubs. ecDNA hubs persist without transcription and are tethered by BET protein BRD4. BET inhibitor JQ1 disperses ecDNA hubs, preferentially inhibits ecDNA oncogene transcription, and kills ecDNA+ cancer cells. Two amplified oncogenes MYC and FGFR2 intermix in ecDNA hubs, engage in intermolecular enhancer-promoter interactions, and transcription is uniformly sensitive to JQ1. Thus, ecDNA hubs are nuclear bodies of many ecDNAs tethered by proteins and platforms for cooperative transcription, leveraging the power of oncogene diversification and combinatorial DNA interactions. We suggest ecDNA hubs, rather than individual ecDNAs, as units of oncogene function, cooperative evolution, and new targets for cancer therapy.
(g) A schematic diagram of the proposed ecDNA hub 594model for intermolecular cooperation.
Rooting the animal tree of life
There has been considerable debate about the placement of the root in the animal tree of life, which has emerged as one of the most challenging problems in animal phylogenetics. This debate has major implications for our understanding of the earliest events in animal evolution, including the origin of the nervous system. Some phylogenetic analyses support a root that places the first split in the phylogeny of living animals between sponges and all other animals (the Porifera-sister hypothesis), and others find support for a split between comb jellies and all other animals (Ctenophora-sister). These analyses differ in many respects, including in the genes considered, species considered, molecular evolution models, and software. Here we systematically explore the rooting of the animal tree of life under consistent conditions by synthesizing data and results from 15 previous phylogenomic studies and performing a comprehensive set of new standardized analyses. It has previously been suggested that site-heterogeneous models favor Porifera-sister, but we find that this is not the case. Rather, Porifera-sister is only obtained under a narrow set of conditions when the number of site-heterogeneous categories is unconstrained and range into the hundreds. Site-heterogenous models with a fixed number of dozens of categories support Ctenophora-sister, and cross-validation indicates that such models fit the data just as well as the unconstrained models. Our analyses shed light on an important source of variation between phylogenomic studies of the animal root. The datasets and analyses consolidated here will also be a useful test-platform for the development of phylogenomic methods for this and other difficult problems.
Universal annotation of the human genome through integration of over a thousand epigenomic datasets
Genome-wide maps of chromatin marks such as histone modifications and open chromatin sites provide valuable information for annotating the non-coding genome, including identifying regulatory elements. Computational approaches such as ChromHMM have been applied to discover and annotate chromatin states defined by combinatorial and spatial patterns of chromatin marks within the same cell type. An alternative ‘stacked modeling’ approach was previously suggested, where chromatin states are defined jointly from datasets of multiple cell types to produce a single universal genome annotation based on all datasets. Despite its potential benefits for applications that are not specific to one cell type, such an approach was previously applied only for small-scale specialized purposes. Large-scale applications of stacked modeling have previously posed scalability challenges. In this paper, using a version of ChromHMM enhanced for large-scale applications, we applied the stacked modeling approach to produce a universal chromatin state annotation of the human genome using over 1000 datasets from more than 100 cell types, denoted the full-stack model. The full-stack model states show distinct enrichments for external genomic annotations, which we used in characterizing each state. Compared to cell-type-specific annotations, the full-stack annotation directly differentiates constitutive from cell-type-specific activity and is more predictive of locations of external genomic annotations. Overall, the full-stack ChromHMM model provides a universal chromatin state annotation of the genome and a unified global view of over 1000 datasets. We expect this to be a useful resource that complements existing cell-type-specific annotations for studying the non-coding human genome.
An ancient coronavirus-like epidemic drove adaptation in East Asians from 25,000 to 5,000 years ago
The current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors – pointing to which viruses have future pandemic potential. Here, we apply evolutionary analyses to human genomic datasets to recover selection events involving tens of human genes that interact with coronaviruses, including SARS-CoV-2, that started 25,000 years ago. These adaptive events were limited to ancestral East Asian populations, the geographical origin of several modern coronavirus epidemics. An arms race with an ancient corona-like virus may thus have taken place in ancestral East Asian populations. By learning more about our ancient viral foes, our study highlights the promise of evolutionary information to combat the pandemics of the future.
6.【质谱】瑞士苏黎世大学（University of Zurich）：使用R语言轻松对质谱原始数据进行操作
rawR - Direct access to raw mass spectrometry data in R
The Bioconductor project has shown that the R statistical environment is a highly valuable tool for genomics data analysis1, but with respect to proteomics we are still missing low level infrastructure to enable performant and robust analysis workflows in R. Fundamentally important are libraries that provide raw data access. Our R package rawDiag has provided the proof-of-principle how access to mass spectromerty raw files can be realized by wrapping vendor-provided APIs, but rather focused on meta data analysis and visualization2. Our novel package rawR now provides complete, OS independent access to all spectral data logged in Thermo Fisher Scientific raw files. In this technical note we present implementation details and describe the main functionality provided by the rawR package. In addition, we report two use cases inspired by real-word research task that demonstrate the application of the package.Availability https://github.com/fgcz/rawR
DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions
G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually 100 mM) K+, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM TMAA. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).
Long read metagenomics, the next step?
Results Here we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads followed by assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. Long reads allow efficient direct retrieval of complete genes (473M/Tb) and operons before assembly, facilitating annotation and compensates the limitations of short reads or short-read assemblies. MetaSPAdes was the most appropriate assembly program when used in combination with short reads. The assemblies of the long reads allow also the reconstruction of much more complete metagenome-assembled genomes, even from microbes with high microdiversity. The flexible genome of reconstructed MAGs is much more complete and allows rescuing more adaptive genes.
Genetic Evidence for Selective Transfer of Microbes Between the International Space Station and an Astronaut
Microbial transfer of both pathogenic and non-pathogenic strains from the environment can influence a person’s health, but such studies are rare and the phenomenon is difficult to study. Here, we use the unique, isolated environment of the International Space Station (ISS) to track environmental movement of microbes in an astronaut’s body. We identified several microbial taxa, including Serratia proteamaculans and Rickettsia australis, which appear to have been transferred from the environment of to the gut and oral microbiomes of the on-board astronaut, and also observed an exchange of genetic elements between the microbial species. Strains were matched at the SNP and haplotype-level, and notably some strains persisted even after the astronaut’s return to Earth. Finally, some transferred taxa correspond to secondary strains in the ISS environment, suggesting that this process may be mediated by evolutionary selection, and thus, continual microbial monitoring can be important to future spaceflight mission planning and habitat design.
10.【补漏】巴黎萨克雷大学Tom Delmont实验室：世界最大海洋微生物组项目Tara Oceans里挖掘到的真核生物宏基因组
Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics
Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion metagenomic reads from 143 Tara Oceans stations to reconstruct and manually curate more than 700 abundant and widespread eukaryotic metagenome-assembled genomes ranging from 10 Mbp to up to 1.3 Gbp. The resulting non-redundant genomic resource of 25 billion nucleotides that describe 10 million genes covers a wide range of poorly characterized unicellular and multicellular eukaryotic lineages that complement the long-standing contributions of culture efforts to survey the tree of marine life while better representing plankton from the open ocean. Phylogeny of the DNA-dependent RNA polymerase placed this genomic resource in a comprehensive evolutionary framework that provided insights into the relationships of eukaryotic supergroups. From there, classification of unicellular eukaryotic plankton based on functions encoded in their genes revealed four major groups connecting distantly related lineages such as the diatoms and green algae. There has been a recurrent problem in understanding the interplay between eukaryotes’ vertical evolution and their phenotype. By disentangling phylogenetic signals from functional trends with genomics, we found that neither the classical trophic mode of plankton nor its vertical evolutionary history could fully explain the genomic functional landscape of marine eukaryotes that coexisted for millions of years.