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opencc-zeroAug 2020View details →

Root associated fungi in Arctic Glacier Forlands raw sequences

Climate change causes Arctic glaciers to retreat faster, exposing new areas for colonization. Several pioneer plants likely to colonize recent deglaciated, nutrient-poor areas depend on fungal partners for successful establishment. Little is known about general patterns or characteristics of facilitating fungal pioneers and how they vary with regional climate in the Arctic. The High Arctic Archipelago Svalbard represents an excellent study system to address these questions, as glaciers cover ∼60% of the land surface and recent estimations suggest at least 7% reduction of glacier area since 1960s. Roots of two ectomycorrhizal (ECM) plants (Salix polaris and Bistorta vivipara ) were sampled in eight glacier forelands. Associated ECM fungi were assessed using DNA metabarcoding. About 25% of the diversity was unknown at family level, indicating presence of undescribed species. Seven genera dominated based on richness and abundance, but their relative importance varied with local factors. The genus Geopora showed surprisingly high richness and abundance, particularly in dry, nutrient-poor forelands. Such forelands will diminish along with increasing temperature and precipitation, and faster succession. Our results support a taxonomical shift in pioneer ECM diversity with climate change, and we are likely to lose unknown fungal diversity, without knowing their identity or ecological importance.

opencc-zeroAug 2020View details →

Data from: Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies

Genomic resources for the domestic dog have improved with the widespread adoption of a 173k SNP array platform and updated reference genome. SNP arrays of this density are sufficient for detecting genetic associations within breeds but are underpowered for finding associations across multiple breeds or in mixed-breed dogs, where linkage disequilibrium rapidly decays between markers, even though such studies would hold particular promise for mapping complex diseases and traits. Here we introduce an imputation reference panel, consisting of 365 diverse, whole-genome sequenced dogs and wolves, which increases the number of markers that can be queried in genome-wide association studies approximately 130-fold. Using previously genotyped dogs, we show the utility of this reference panel in identifying potentially novel associations, including a locus on CFA20 significantly associated with cranial cruciate ligament disease, and fine-mapping for canine body size and blood phenotypes, even when causal loci are not in strong linkage disequilibrium with any single array marker. This reference panel resource will improve future genome-wide association studies for canine complex diseases and other phenotypes.

opencc-zeroApr 2020View details →

The genome sequence of Samia ricini, a new model species of lepidopteran insect

Samia ricini, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Since S. ricini is much more tough and resistant to diseases than the current model species Bombyx mori, the former can be easily reared compared to the latter. In addition, genetic resources available for S. ricini rival or even exceed those for B. mori: at least 26 eco-races of S. ricini are reported and S. ricini can hybridize with wild Samia species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour, larval spot pattern, etc. are different between S. riciniand wild Samia species so that those traits can be the target for forward genetic analysis. In order to facilitate genetic research in S. ricini, we determined the whole genome sequence of S. ricini. The assembled genome of S. ricini was 458 Mb with 155 scaffolds, and the N50 length of the assembly was approximately 21 Mb. 16,702 protein coding genes were predicted in the assembly. Although the gene repertoire of S. ricini was not so different from that of B. mori, some genes, such as chorion genes and fibroin genes, seemed to have specifically evolved in S. ricini.

opencc-by-4.0Sep 2020View details →

Multiple sequence alignment of DNA-A sequences from ACMBFV, ACMV, CMMGV, EACMCV, EACMKV, EACMMV, EACMV, EACMZV, SACMV, ICMV, SLCMV (11 species)

All full-length DNA-A sequences available in GenBank as of July 2019 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were manually adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).

opencc-by-4.0Sep 2020View details →

Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms

Supplementary materials for the porcine astrovirus study in East Africa. Table S1: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank  Table S2. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega Table S3. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega Table S4: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains. Table S5. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software

opencc-zeroAug 2020View details →

House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences

<div> The Eurasianhouse mouse Mus musculusis useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far asthe Japanese Archipelagofrom their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: 1) broad spatial expansion into eastern Europe and the western part of western China, 2) dispersal to the eastern part of western China, 3) dispersal tonorthern China, 4) dispersal to the Korean Peninsula and 5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2,000–18,000 years. The dispersal of CAS was characterised by three events: initial divergences(ca. 7,000–9,000 years ago) of haplogroups in northern most China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basinto broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4,000–6,000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2,000–3,500). This study provides a solid framework for the spatiotemporal movementof the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration. </div>

opencc-zeroSep 2020View details →

Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling

In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. Instead of lineage-specific duplications, we found that bat V1rs in bats show high levels of orthology to those of their relatives, and receptors are under comparative levels of purifying selection compared to non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggest roles other than conspecific recognition or mating initiation in social behavior.

opencc-zeroSep 2020View details →

Psocodea Phylogenomic dataset from: Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

This dataset includes all alignments used for the phylogenomic analysis of Psocodea. In this dataset, includes all result files of phylogenomic analyses completed. This includes maximum likelihood, astral, MCMCtree, quartet sampling, and all gene trees. Any relevant input files are included, and any materials are available upon request. The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

Assigning the sex-specific markers via genotyping-by-sequencing onto the Y chromosome for a torrent frog Amolops mantzorum

We use a genotyping-by-sequencing (GBS) approach to identify sex-linked markers in a torrent frog (Amolops mantzorum) using wild-caught individuals of 21 males and 19 females from the same population. A total of 141 putatively sex-linked markers were screened from 1,015,964 GBS tags through three approaches, respectively based on sex differences in allele frequencies, sex difference in heterozygosity, and sex-limited occurrence. With validations, 69 sex-linked markers were confirmed, all of which point to male heterogamety. The male specificity of eight sex markers was further verified by PCR amplifications with a large number of additional individuals covering the whole geographic distribution of the species. Y chromosome (No. 5) was microdissected under a light microscope, amplified by whole-genome amplification, and assembled a draft Y genome. 55 out of 69 sex-linked markers could be mapped to the Y chromosome assembly (i.e 79.7 %). Thus the chromosome 5 could be added as candidate chromosomes that particularly favored to recruit for sex determination than others among frogs. Three sex-linked markers that mapped on Y chromosome were aligned to three different promoter regions of Rana rugosa CYP19A1 gene, which might be considered as a candidate gene to trigger sex determination in A. mantzorum.

The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population

Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare and an indica variety 9311 was utilized to study the genetic base of TRD. A total of eighteen genomic regions were identified for TRD in the BILs. Among them, twelve and six regions showed indica (9311) and japonica (Nipponbare) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from inter-subspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intra-subspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking inter-subspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the inter-subspecific hybrid breeding programs.

opencc-zeroDec 2019View details →

Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix

Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral, Seriatopora hystrix were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. Seriatopora hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa.As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones.Based on microsatellite analyses three groups could be distinguished within the WIO: (I) north Madagascar, (II) south-west Madagascar together with one site in northern Mozambique (Nacala), and (III) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of S. hystrix, and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.

SNPs markers of Trypoxylus dichotomus developed by using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques

The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific‐locus amplified fragment sequencing (SLAF‐seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping.

An evaluation of inbreeding measures using a whole genome sequenced cattle pedigree

The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies. The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighbouring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus specific homozygosity.

opencc-by-4.0Nov 2020View details →

Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences

Abstract for overall study: The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence. Specific description for this dataset: We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera. The transciptomes of  senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.

opencc-by-4.0Oct 2020View details →

Detection of fusion transcripts and their genomic breakpoints from RNA sequencing data - Table S03 - All detected SVs.xlsx

Large concatenated results table on all samples of the Dr. Disco study.

opencc-zeroNov 2020View details →

SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq)

Our study is the first to explore the genetic composition of ancient Cryptomeria trees across distribution range in China. Background and Objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and Methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal lower genetic variation but higher genetic differentiation (Ho=0.143, FST=0.1204) than Japanese Cryptomeria (Ho=0.245, FST=0.0455). The 86% within-population variation is based on analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. STRUCTURE analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. Demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species' unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.

opencc-by-4.0Nov 2020View details →

The new Garba Guracha palynological sequence: revision and data expansion

Dataset by Graciela Gil-Romera et al. submitted to "Palaeocology of Africa". dictionary.csv is the file containing information on how taxa are attibuted to different functional and bioclimatic types and pollen.csv contains all raw pollen data. Charcoal data presented in Fig3 can be downloaded from here: https://github.com/ggilromera/BaleFire The age-depth model has been built using the dates and code published here: https://link.springer.com/article/10.1007/s10933-020-00138-w#Sec36 And the raw and calibrated dated samples can be found in the supmat_bittner_etal_2020.docx file.

opencc-by-4.0Jan 2021View details →

Urban wastewater virome by viral metagenomics and target enrichment sequencing

Metagenomic analysis of virus in raw sewage.

opennotspecifiedDec 2001View details →

................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup. in Bartonella schoenbuchii sp. nov., isolated from the blood of wild roe deer.

................................................................................................................................................. Fig. 5. Phylogenetic tree based on 16S rRNA sequences (a) and gltA sequences (b) showing the position of strains R1T, R3, R4 and R6 in relation to the known Bartonella spp. The tree was rooted by using Brucella abortus (a) and Sinorhizobium meliloti (b) as the outgroup.