Transcriptome analysis of Paecilomyces hepiali at different growth stages and culture additives to reveal putative genes in cordycepin biosynthesis.

Paecilomyces hepialid (PH) is an endoparasitic fungus of Cordyceps sinensis (CS) and has become a substitute for CS due to their similar pharmacological activities. Because the market demand for CS is difficult to satisfy, and cordycepin, the effective compound of CS, is difficult to industrially produce, we produced 5 samples of PH by culturing for different durations and adding different additives to the culture broth, and detected their cordycepin content with UPLC ESI MS/MS. Then we grouped these cultures into five transcriptome comparisons containing 3 time variable groups and 2 additive variable groups. We used next-generation (NG) sequencing methods to acquire transcriptomic information and investigated the response of gene expression to the additives and the influence of different growth stages. This work will contribute to a better understanding of purine metabolism in PH, and possibly in other Cordyceps species. It will provide a useful resource to further advance transcriptomics studies in Cordyceps species.

DNA repair and replication links to pluripotency and differentiation capacity of pig iPS cells.

Pigs are proposed to be suitable large animal models for test of the efficacy and safety of induced pluripotent stem cells (iPSCs) for stem cell therapy, but authentic pig ES/iPS cell lines with germline competence are rarely produced. The pathways or signaling underlying the defective competent pig iPSCs remain poorly understood. By improving induction conditions using various small chemicals, we generated pig iPSCs that exhibited high pluripotency and differentiation capacity that can contribute to chimeras. However, their potency was reduced with increasing passages by teratoma formation test, and correlated with declined expression levels of Rex1, an important marker for naïve state. By RNA-sequencing analysis, genes related to WNT signaling were upregulated and MAPK signaling and TGFß pathways downregulated in pig iPSCs compared to fibroblasts, but they were abnormally expressed during passages. Notably, pathways involving in DNA repair and replication were upregulated at early passage, but downregulated in iPSCs during prolonged passage in cluster with fibroblasts. Our data suggests that reduced DNA repair and replication capacity links to the instability of pig iPSCs. Targeting these pathways may facilitate generation of truly pluripotent pig iPSCs, with implication in translational studies.

The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes).

Paecilomyces hepiali, belonging to the Eurotiales order Ascomycota, is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. Here, we report the complete mitochondrial DNA sequences of P. hepiali for the first time. The genome is 24,245 bp in length, encoding 15 protein-coding genes (PCGs), 2 rRNA genes, 25 tRNA genes and 3 homing endonucleases. The overall AT composition is 73.37% and the average AT content of PCG, rRNA, tRNA and non-coding region are 74.21%, 66.07%, 62.83% and 75.96%, respectively. Phylogenetic analysis with eight Ascomycota species and thirteen Basidiomycota species revealed that P. hepiali is was more closely related to Cordyceps bassiana, Cordycep smilitaris and Cordyceps brongniartii. It is confirmed that P. hepiali is a derivative of Cordyceps sinensis. This study provided valuable information on the gene contents of the mitochondrial genome and would facilitate the study of function and evolution of P. hepiali.

Genome sequence and genetic diversity of the common carp, Cyprinus carpio.

The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb.

BACKGROUND: Traditional Chinese medicine uses various herbs for the treatment of various diseases for thousands of years and it is now time to assess the characteristics and effectiveness of these medicinal plants based on modern genetic and molecular tools. The herb Flos Lonicerae Japonicae (FLJ or Lonicera japonica Thunb.) is used as an anti-inflammatory agent but the chemical quality of FLJ and its medicinal efficacy has not been consistent. Here, we analyzed the transcriptomes and metabolic pathways to evaluate the active medicinal compounds in FLJ and hope that this approach can be used for a variety of medicinal herbs in the future. RESULTS: We assess transcriptomic differences between FLJ and L. japonica Thunb. var. chinensis (Watts) (rFLJ), which may explain the variable medicinal effects. We acquired transcriptomic data (over 100 million reads) from the two herbs, using RNA-seq method and the Illumina GAII platform. The transcriptomic profiles contain over 6,000 expressed sequence tags (ESTs) for each of the three flower development stages from FLJ, as well as comparable amount of ESTs from the rFLJ flower bud. To elucidate enzymatic divergence on biosynthetic pathways between the two varieties, we correlated genes and their expression profiles to known metabolic activities involving the relevant active compounds, including phenolic acids, flavonoids, terpenoids, and fatty acids. We also analyzed the diversification of genes that process the active compounds to distinguish orthologs and paralogs together with the pathways concerning biosynthesis of phenolic acid and its connections with other related pathways. CONCLUSIONS: Our study provides both an initial description of gene expression profiles in flowers of FLJ and its counterfeit rFLJ and the enzyme pool that can be used to evaluate FLJ quality. Detailed molecular-level analyses allow us to decipher the relationship between metabolic pathways involved in processing active medicinal compounds and gene expressions of their processing enzymes. Our evolutionary analysis revealed specific functional divergence of orthologs and paralogs, which lead to variation in gene functions that govern the profile of active compounds.