Project description:This is an auto-generated model with COBRA Matlab toolbox. The gadMorTrinigy de novo Trinity transcript assembly and peptide sequences are available at https://doi.org/10.6084/m9.figshare.c.5168303.v2
Project description:Studies of the gene expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of unigenes from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 51716 unigenes were identified based on four mRNA libraries. 2044 unigenes were differentially expressed between adolescence and juvenile sika deer, 1946 unigenes were differentially expressed between adult and adolescence sika deer, and 2209 unigenes were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that DE unigenes were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that Myh1, Myh2, Myh7, ACTN3 etc. may play important roles in muscle growth and development, and WWP1, DEK, UCP3, FUS etc. may have key roles in muscle aging. In this study, we determined the dynamic unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.
Project description:Studies of the miRNA expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the differential expression of miRNAs from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 171 known miRNAs and 60 novel miRNAs were identified based on four small RNA libraries. 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 4 miRNAs were differentially expressed between adult and adolescence sika deer, and 1 miRNAs were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that miRNA were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that miR-133a, miR-133c, miR-192, miR-151-3p etc. may play important roles in muscle growth and development, and miR-17-5p, miR-378b, miR-199a-5p, miR-7 etc. may have key roles in muscle aging. In this study, we determined the dynamic miRNA in muscle tissue for the first time in sika deer. The age-dependent miRNAs identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.
Project description:We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90nt were generated. Totally 48,768 unigenes (mean size = 488 bp) were assembled through transcriptome de novo assembly, which represent more than 3-fold of all the sequences of Hevea brasiliensis deposited in the GenBank. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. Total 37,373 unigenes were successfully annotated and more than 10% of unigenes were aligned to known proteins of Euphorbiaceae. The unigenes contain nearly complete collection of known rubber-synthesis-related genes. Our data provides the most comprehensive sequence resource available for study rubber tree and demonstrates the availability of Illumina sequencing and de novo transcriptome assembly in a species lacking genome information. The transcriptome of latex and leaf in Hevea brasiliensis