Function annotation of Takifugu flavidus genome genes

Function annotation ressult of Takifugu flavidus genome gene

annotation of Opniocepnalus argus var Kimnra genome

Annotation files of Opniocepnalus argus var Kimnra genom

gff of Opniocepnalus argus Var Kimnra genome

Gff file of Opniocepnalus argus Var Kimnra genom

Genome annotation of Trilophysa bleekeri

These are the gene structure and function annotation file of Trilophysa bleekeri

A New Transferable Forcefield for Simulating the Mechanics of CaCO₃ Crystals

Many sets of forcefield parameters for calcium carbonate (CaCO3) and CaCO3–water interactions have been developed for thermodynamic calculations, but growing interest in modeling the molecular-scale mechanics of biomineral nanocomposite materials such as nacre has led to a need for interaction parameters that accurately model the anisotropic mechanical properties of CaCO3. A novel forcefield for aragonite, one polymorph of CaCO3, has been fitted to the structure and elastic constants of the mineral, and the validation of these interaction parameters demonstrates that the forcefield can well capture the shear and elastic moduli of aragonite and also performs well when transferred to other CaCO3 polymorphs. The corresponding aragonite–water and aragonite–protein parameters are also obtained and utilized in force probe molecular dynamics (FPMD) simulations of the forced desorption of an acidic polypeptide from an aragonite crystal surface, resulting in a rupture force of roughly 60 pN per amino acid residue at pulling speeds characteristic of Atomic Force Microscope experiments. Our forcefield for CaCO3 and CaCO3–protein interactions can be applied to study the physical and mechanical properties of organic–inorganic composite systems, especially for the next generation of bionanocomposite materials

The annotation of comprehensive transcriptome for endemic Schizothoracinae fish in the Tibetan Plateau

The annotation of comprehensive transcriptome for endemic Schizothoracinae fish in the Tibetan Platea

DataSheet_1_Rediscover and Refine QTLs for Pig Scrotal Hernia by Increasing a Specially Designed F3 Population and Using Whole-Genome Sequence Imputation Technology.pdf

Pig scrotal hernia is one of the most common congenital defects triggered by both genetic and environmental factors, leading to severe economic loss as well as poor animal welfare in the pig industry. Identification and implementation of genomic regions controlling scrotal hernia in breeding is of great appeal to reduce incidences of hernia in pig production. The aim of this study was to identify such regions or molecular markers affecting scrotal hernia in pigs. First of all, we summarized and analyzed the results of some international teams on scrotal hernia and designed a specially population which contains 246 male individuals. We then performed genome-wide association study (GWAS) in this specially designed population using two scenarios, i.e., the target panel data before and after imputation, which contain 42,365 SNPs and 18,756,672 SNPs, respectively. In addition, a series of methods including genetic differentiation analysis, linkage disequilibrium and linkage analysis (LDLA), and haplotype sharing analysis were appropriate to provide for further analysis to identify the potential gene underlying the QTL. The GWAS in this report detected a highly significant region affecting scrotal hernia within a 24.8Mb region (114.1–138.9Mb) on SSC8. And the result of genetic differentiation analysis also showed a strong genetic differentiation signal between 116.1 and 132.7Mb on SSC8. In addition, the QTL interval was refined to 2.99Mb by combining LDLA and genetic differentiation analysis. Finally, two susceptibility haplotypes were identified through haplotype sharing analysis, with one potential causal gene in it. Our study provided deeper insights into the genetic architecture of pig scrotal hernia and contributed to further fine-mapping and characterize haplotype and gene that influence scrotal hernia in pigs.</p

Table_3_Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae.xls

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.</p

Data_Sheet_1_Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae.docx

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.</p

Table_4_Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae.xlsx

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.</p