Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb ...genome se- quences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16- epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.
Understanding soybean (Glycine max) domestication and improvement at a genetic level is important to inform future efforts to further improve a crop that provides the world's main source of oilseed. ...We detect 230 selective sweeps and 162 selected copy number variants by analysis of 302 resequenced wild, landrace and improved soybean accessions at >11× depth. A genome-wide association study using these new sequences reveals associations between 10 selected regions and 9 domestication or improvement traits, and identifies 13 previously uncharacterized loci for agronomic traits including oil content, plant height and pubescence form. Combined with previous quantitative trait loci (QTL) information, we find that, of the 230 selected regions, 96 correlate with reported oil QTLs and 21 contain fatty acid biosynthesis genes. Moreover, we observe that some traits and loci are associated with geographical regions, which shows that soybean populations are structured geographically. This study provides resources for genomics-enabled improvements in soybean breeding.
Summary
1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for ...auditing by neutral parties, which is necessary for dispute resolution.
2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass‐PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’.
3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within‐community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding.
4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.
Presentation
Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows ...positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF₁. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF₂ hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
Despite widespread recognition of its great promise to aid decision‐making in environmental management, the applied use of metabarcoding requires improvements to reduce the multiple errors that arise ...during PCR amplification, sequencing and library generation. We present a co‐designed wet‐lab and bioinformatic workflow for metabarcoding bulk samples that removes both false‐positive (tag jumps, chimeras, erroneous sequences) and false‐negative (‘dropout’) errors. However, we find that it is not possible to recover relative‐abundance information from amplicon data, due to persistent species‐specific biases.
To present and validate our workflow, we created eight mock arthropod soups, all containing the same 248 arthropod morphospecies but differing in absolute and relative DNA concentrations, and we ran them under five different PCR conditions. Our pipeline includes qPCR‐optimized PCR annealing temperature and cycle number, twin‐tagging, multiple independent PCR replicates per sample, and negative and positive controls. In the bioinformatic portion, we introduce Begum, which is a new version of DAMe (Zepeda‐Mendoza et al., 2016. BMC Res. Notes 9:255) that ignores heterogeneity spacers, allows primer mismatches when demultiplexing samples and is more efficient. Like DAMe, Begum removes tag‐jumped reads and removes sequence errors by keeping only sequences that appear in more than one PCR above a minimum copy number per PCR. The filtering thresholds are user‐configurable.
We report that OTU dropout frequency and taxonomic amplification bias are both reduced by using a PCR annealing temperature and cycle number on the low ends of the ranges currently used for the Leray‐FolDegenRev primers. We also report that tag jumps and erroneous sequences can be nearly eliminated with Begum filtering, at the cost of only a small rise in dropouts. We replicate published findings that uneven size distribution of input biomasses leads to greater dropout frequency and that OTU size is a poor predictor of species input biomass. Finally, we find no evidence for ‘tag‐biased’ PCR amplification.
To aid learning, reproducibility, and the design and testing of alternative metabarcoding pipelines, we provide our Illumina and input‐species sequence datasets, scripts, a spreadsheet for designing primer tags and a tutorial.
摘要
高通量条形码在环境保护和管理相关决策研究中的适用性已获得广泛的共识, 但是若要在更广的领域应用该方法, 还需要进一步减少PCR扩增、文库构建以及测序所带来的错误和偏好。本研究设计了一种针对混合生物样本的高通量条形码流程, 这一流程改进了高通量条形码的实验设计和生物信息学分析, 能减少结果中的假阳性 (如标签错配、嵌合体、错误序列) 和假阴性。研究结果还显示, 由于不同物种的扩增效率存在差异, 因此基于扩增子数据的高通量条形码并不能获取准确的物种定量信息。
本研究人为构建了8个生物多样性汤——节肢动物的混合样本, 每一个汤中都含有同样的248个节肢动物的形态种, 它们的DNA被以不同的浓度比例混入这8个汤中。然后这8个汤在5种不同的PCR条件下被扩增。本研究采用双胞胎标记法来双向标记引物, 每个样本都进行多次独立的PCR扩增, 每一批次的PCR扩增都包含阳性与阴性对照, 并且我们通过qPCR来优化高通量条形码PCR最终使用的退火温度和循环数。在生物信息学分析部分, 我们采用的是Begum (Zepeda Mendoza等发表的DAMe的改进版, 2016. BMCRes. Notes 9:255) , 它在样本拆分时可以忽略为了测序中平衡碱基而添加在标签上的几个碱基, 并允许引物序列的错配, 且提高了运算速率。Begum能去除由于标签跳动所产生的假阳性序列, 以及通过设置多个PCR重复和某一序列的重复出现次数来过滤PCR和测序等产生的错误序列。
本研究结果显示, 在使用Leray‐Fol‐Degen‐Rev的引物对扩增时, 采取较低的退火温度和循环数能有效提高OTU得率, 及减少扩增偏好性。本研究还发现Begum能过滤掉几乎所有的标签跳动和错误序列。我们再次证实了样本中物种生物量的不均衡会导致结果中更多的物种信息丢失, 而且OTU的序列数并不能直接用于指示物种的生物量。最后, 研究结果表明在优化的PCR条件下, 并未产生明显的标签偏好现象 (即由连接引物的标签不同而引发的PCR扩增偏好) 。
为了让更多人能学习、验证、并设计适合自己的高通量条形码流程, 我们提供了本文中用于构建生物多样性汤所有物种的序列、Illumina测序数据、完整的分析命令脚本, 以及用于引物标签设计的表格和指南。
Identifying and protecting hotspots of endemism and species richness is crucial for mitigating the global biodiversity crisis. However, our understanding of spatial diversity patterns is far from ...complete, which severely limits our ability to conserve biodiversity hotspots. Here, we report a comprehensive analysis of amphibian species diversity in China, one of the most species-rich countries on Earth. Our study combines 20 y of field surveys with new molecular analyses of 521 described species and also identifies 100 potential cryptic species. We identify 10 hotspots of amphibian diversity in China, each with exceptional species richness and endemism and with exceptional phylogenetic diversity and phylogenetic endemism (based on a new time-calibrated, species-level phylogeny for Chinese amphibians). These 10 hotspots encompass 59.6% of China's described amphibian species, 49.0% of cryptic species, and 55.6% of species endemic to China. Only four of these 10 hotspots correspond to previously recognized biodiversity hotspots. The six new hotspots include the Nanling Mountains and other mountain ranges in South China. Among the 186 species in the six new hotspots, only 9.7% are well covered by protected areas and most (88.2%) are exposed to high human impacts. Five of the six new hotspots are under very high human pressure and are in urgent need of protection. We also find that patterns of richness in cryptic species are significantly related to those in described species but are not identical.
Vertebrate evolution was accompanied by two rounds of whole-genome duplication followed by functional divergence in terms of regulatory circuits and gene expression patterns. As a basal and ...slow-evolving chordate species, amphioxus is an ideal paradigm for exploring the origin and evolution of vertebrates. Single-cell sequencing has been widely used to construct the developmental cell atlas of several representative species of vertebrates (human, mouse, zebrafish, and frog) and tunicates (sea squirts). Here, we perform single-nucleus RNA sequencing (snRNA-seq) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) for different stages of amphioxus (covering embryogenesis and adult tissues). With the datasets generated, we constructed a developmental tree for amphioxus cell fate commitment and lineage specification and characterize the underlying key regulators and genetic regulatory networks. The data are publicly available on the online platform AmphioxusAtlas.
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•A snRNA-seq atlas of amphioxus developmental embryos and multiple adult tissues•A scATAC-seq atlas of amphioxus developmental embryos•A developmental tree for amphioxus cell fate commitment and lineage specification•Computational identification and validation of lineage-specific markers
Ma et al. conduct a joint profiling of gene expression and chromatin accessibility during amphioxus embryogenesis at single-cell resolution. With the datasets generated, a developmental tree for amphioxus cell fate commitment and lineage specification is constructed, and multiple markers for each lineage are identified and validated.
The process of domestication has led to dramatic differences in behavioral traits between domestic dogs and gray wolves. Whole-genome research found that a class of putative positively selected genes ...were related to various aspects of learning and memory, such as long-term potentiation and long-term depression. In this study, we constructed a single-nucleus transcriptomic atlas of the dog hippocampus to illustrate its cell types, cell lineage and molecular features. Using the transcriptomes of 105 057 nuclei from the hippocampus of a Beagle dog, we identified 26 cell clusters and a putative trajectory of oligodendrocyte development. Comparative analysis revealed a significant convergence between dog differentially expressed genes (DEGs) and putative positively selected genes (PSGs). Forty putative PSGs were DEGs in glutamatergic neurons, especially in Cluster 14, which is related to the regulation of nervous system development. In summary, this study provides a blueprint to understand the cellular mechanism of dog domestication.
To date, the sensitivity of currently available biomarkers based on the methylation of gene promoters is suboptimal for detecting adenomas and early-stage colorectal cancer (CRC). We aimed to develop ...biomarkers with methylated DNA binding sites of the multifunctional transcriptional factor CTCF for early detection of CRC. Using combined analyses of genome-wide occupation and the methylation profile of CTCF-binding sites, we identified candidate CTCF-binding sites. Then, we applied methylation-sensitive high-resolution melting (MS-HRM) and mass spectrometry analysis to screen and validate these candidate sites in diverse sample sets. We identified a set of colorectal neoplasia-specific biomarkers with robust performance. The top five biomarkers were selected and recommended for early detection of colorectal neoplasia. All of the five novel biomarkers exhibited a more robust discriminatory performance than that by
and
, two currently acknowledged robust methylation biomarkers. When the five new biomarkers were considered as a marker panel and tumor-positive was defined as having two or more (of the five) positive biomarkers, the marker panel could achieve a sensitivity of 91.67% for adenomas, 97.44% for Stage I CRC, 94.06% for Stage II CRC, 93.62% for Stage III CRC, and 93.54% for total colorectal tumors with a specificity of 94.05%. To our knowledge, this is the first study for colorectal neoplasia-specific methylation biomarkers based on CTCF-binding sites. Using a similar strategy, CTCF-binding sites could be potentially developed into biomarkers for other tumors. In summary, this study opens a new area in developing biomarkers for tumor prevention and treatment.
In China, the majority of ovarian cancer patients (80%–90%) are women who are diagnosed with epithelial ovarian cancer. The SYNPO2 gene has recently been reported to be associated with epithelial ...ovarian cancer in Europeans. To investigate the association of common variants of SYNPO2 gene with epithelial ovarian cancer in Han Chinese individuals, we designed a case–control study with 719 epithelial ovarian cancer patients and 1568 unrelated healthy controls of Han Chinese descent. A total of 49 tagging single-nucleotide polymorphisms were genotyped; single-single-nucleotide polymorphism association, imputation, and haplotypic association analyses were performed. The single-nucleotide polymorphism rs17329882 was found to be strongly associated with serous epithelial ovarian cancer and with ages ≤49 years, consistent with the pre-menopausal status of analyzed epithelial ovarian cancer cases. Odds ratios and 95% confidence intervals provided evidence of the risk effects of the C allele of the single-nucleotide polymorphism on epithelial ovarian cancer. Imputation analyses also confirmed the results with a similar pattern. Additionally, haplotype analyses indicated that the haplotype block that contained rs17329882 was significantly associated with epithelial ovarian cancer risk, specifically with the serous epithelial ovarian cancer subtype. In conclusion, our results show that SYNPO2 gene plays an important role in the etiology of epithelial ovarian cancer, suggesting that this gene may be a potential genetic modifier for developing epithelial ovarian cancer.
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