Early post-implantation development, especially gastrulation in primates, is accompanied by extensive drastic chromatin reorganization, which remains largely elusive.
To delineate the global chromatin landscape and understand the molecular dynamics during this period, single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) was applied to in vitro cultured monkey embryos to investigate the chromatin status. We delineated the cis-regulatory interactions and identified the regulatory networks and key transcription factors involved in epiblast (EPI), hypoblast, and trophectoderm (TE)/trophoblast lineage specification. We also identified the opposing roles of FGF and BMP signaling in pluripotency regulation in EPI cells. The integrative analysis of chromatin accessibility and gene expression revealed that chromatin status activation precedes gene expression during EPI and trophoblast specification. Finally, we revealed the similarity between EPI and TE in terms of gene expression patterns and demonstrated that NR2F2 and PATZ1 are involved in EPI and trophoblast specification during monkey post-implantation development.
Our findings provide new resources and insights into dissecting the transcriptional regulatory machinery during primate post-implantation development.

With more than 30,000 species, fish are the largest and most ancient vertebrate group. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable use of fish. Here, we announce the Fish10K project, an international collaborative effort aiming to sequence 10,000 representative fish genomes in a systematic manner within ten years, and officially welcome collaborators to join this effort. As a step towards this goal, we herein describe the best practices for the procurement and storage of biospecimens, sequencing, and assembly strategies. To illustrate, we present the genomes of ten fish species from a cohort of 105 species chosen for technology development.

The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.
Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e. 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes.
These data bring new insights into functions, carbohydrate-degrading enzymes and microbes of the rumen that is complementing the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data is made available.

Human urine is traditionally considered to be sterile, and whether the urine harbors distinct microbial communities has been a matter of debate. Potential link between female urine and reproductive tract microbial communities is currently not clear.
Here we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the female reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women.
Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.

Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution and functional studies. Here, we present a quail genome assembly spanning 1.04Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and two sex chromosomes Z/W). Our genomic data has resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey) and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSH), which is correlated with different FSH levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. This study provided a high-quality quail reference genome, identified quail-specific genes and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary process within the Phasianidae family.

Siamese fighting fish Betta splendens are notorious for their aggressiveness and accordingly have been widely used to study aggression. However, the lack of a reference genome has so far limited the understanding of the genetic basis of aggression in this species. Here we present the first reference genome assembly of the Siamese fighting fish.
We first sequenced and de novo assembled a 465.24 Mb genome for the B. splendens variety Giant, with a weighted average (N50) scaffold size of 949.03 Kb and an N50 contig size of 19.01 Kb, covering 99.93% of the estimated genome size. To obtain a chromosome-level genome assembly, we constructed one Hi-C library and sequenced 75.24 Gb reads using the BGISEQ-500 platform. We anchored approximately 93% of the scaffold sequences into 21 chromosomes and evaluated the quality of our assembly using the high contact frequency heatmap and BUSCO. We also performed comparative chromosome analyses between Oryzias latipes and B. splendens, revealing a chromosome conservation evolution in B. splendens. We predicted a total of 23,981 genes assisted by RNA-seq data generated from brain, liver, muscle and heart tissues of Giant, and annotated 15% repetitive sequences in the genome. Additionally, we resequenced other five B. splendens varieties and detected ~3.4M single-nucleotide variations (SNVs) and 27,305 indels.
We provide the first chromosome-level genome for the Siamese fighting fish. The genome will lay a valuable foundation for future research on aggression in B. splendens.

Bamboo is one of the most important non-timber forest products worldwide. However, a chromosome-level reference genome is lacking, and the evolutionary landscape of alternative splicing (AS) in bamboo remains unclear despite emerging data and improved technologies. Here, we provide a chromosome-level de novo genome assembly of the moso bamboo (Phyllostachys edulis) using additional abundance data and different assembly strategies. The significantly improved genome is a Scaffold N50 of 79.90 Mb, approximately 243 times longer than the previous version, and 51,074 high-quality protein-coding loci with intact structures were identified using single-molecule real-time sequencing and manual verification. Moreover, we provide a comprehensive AS profile based on the identification of 266,771 uniform AS events in 25,225 AS genes by large-scale transcriptomic sequencing of 26 representative bamboo tissues using both the Illumina and PacBio sequencing platforms. Via comparison with orthologous genes in related plants, we observed dramatic evolutionary characteristics, suggesting that the AS genes are concentrated in more conserved genes that tend to accumulate higher expressed transcripts and share less specificity. Furthermore, gene family expansion, abundant AS and positive selection were identified in crucial genes involved in lignin biosynthesis, indicating that moso bamboo's specificity in being a woody plant in the grass family. These fundamental studies provide useful information for future studies performing in-depth analyses of comparative genome and AS features. Additionally, our results highlight a global perspective of AS during evolution and diversification in bamboo.

Laboratory rats such as the Sprague-Dawley (SD) rats are important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report on the first catalog of microbial genes in fecal samples from Sprague-Dawley rats. The catalog was established using 98 fecal samples from 49 SD rats divided in 7 experimental groups collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 base pairs (BP), among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8% and 31% of the genes could be annotated to KEGG orthologous groups (KOs), modules and pathways, respectively. A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. 97% of the functional pathways in the human catalog were present in the rat catalogue underscoring the potential use of rats for biomedical research.

The relationship between dyslipidemia and type 2 diabetes (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized.
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was applied to detect the global lipidome in fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects and 98 individuals with normal glucose tolerance (NGT). Both qualitative and quantitative analyses revealed a gradual change in plasma lipid features going from NGT individuals over prediabetic to T2D individuals with T2D patients exhibiting characteristics close to those in prediabetic individuals, whereas they differed significantly from individuals with NGT. We constructed and validated a random forest (RF) classifier with 28 lipidomic features that effectively discriminated T2D from NGT or prediabetes. The majority of the selected features showed significant correlations with diabetic clinical indices.
Hydroxybutyrylcarnitine was positively correlated with fasting plasma glucose (FPG), 2-hour postprandial glucose (2h-PG), glycated hemoglobin (HbA1c) and insulin resistance index (HOMA-IR), and lysophosphatidylcholines such as LysoPC (18:0), LysoPC (18:1) and LysoPC (18:2) were all negatively correlated with HOMA-IR.

Longan (Dimocarpus longan), an important subtropical fruit, is grown in more than 10 countries of the world. Longan is an edible drupe fruit and source of traditional medicine with polyphenol-rich traits, while tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled.The draft genome (about 471.88 Mb) of a China longan cultivar Honghezi was estimated to contain 31,007 high- quality genes and 261.88 Mb of repetitive sequences. No recent whole-genome wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen-resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3H, ANR, and UFGT) and contracted (PAL, CHS, and F35H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine- rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, and the recent expansion and contraction of the NBS-LRR family suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen- resistance characteristics.