Characterization Of Transcriptome In Leg Muscle Of Meat Rabbit In Different Growth Stages

Long non-coding RNA(IncRNA),a class of non-coding RNAs,are longer than 200 nucleotides that don't encode protein and express with tissue specificity and temporal specificity.Previous studies showed that long non-coding RNA also had been involved in many biological processes,such as the activation and inference of transcription,chromosome dosage compensation effect,genomic imprinting,translational regulation and developmental regulation etc.Recently,a kind of non-coding RNAs(circRNAs)with special structure were found to widely existed in animal cells and mostly in the exon's region.Rabbit skeletal muscle is a highly heterogeneous tissue,of which the leg muscle is the great economic value and always the research emphasis of molecular breeding and development of rabbit.With the development and application of molecular biology and bioinformatics,it is possible to reveal the fundamental mechanism of the produce performance of rabbit.It is particularly important to look for the genetic markers associated with meat quality traits.However,the identification or function analysis of IncRNA and circRNA in rabbit hasn't been reported.This study was focused on the study of Zika rabbit and randomly selected nine female rabbits,which were divideded into three groups according to the dates of rabbit(newborn:0 d,50 g,ZKN;5 weeks:35 d,1200 g,ZKY;10 weeks:70 d,1560 g,ZKA.).Then the muscle tissue of right legs was used as the experimental materials.The mRNA,IncRNA and circRNA were selected using transcriptome sequencing technology.Moreover,we analyzed and annoted the differentially expressed mRNAs among different groups,and compared the transcriptome characteristics between mRNAs and IncRNAs.A total of 860 million(855,322,808)reads were identified using the Illumine platform.Under the quality control,850 million(855,322,808)reads with high quality were received.About 87.08%reads of each sample can be blasted to the genome reference by using HISAT.Basing on the blasted reads,56,829 transcripts is obtained after merging the rest of reads.Finally,1129 candidate IncRNAs were identified based on transcript length and expression levels,including 407 new IncRNAs,331 IncRNA transcripts in the intron region,116 IncRNA transcripts in the intergenic,274 overlap and antisense IncRNAs in exon region and 1 overlap and antisense IncRNA in intron region.Candidate IncRNA is distributed on every chromosome with no obvious preference.We identified 56,698 and 927 differentially expressed encoding genes by respectively analysis between ZKY vs ZKA,ZKN vs ZKY and ZKN vs ZKA.These genes were enriched to the pathways of muscle development related such as muscle fiber formation,myosin binding and muscle contraction.The expression of mRNA is both of up-regulated and down-regulated,it suggests that these genes may paly complex regulatory roles in the muscle development of rabbit.A total of 10870 circRNAs were predicted by two prediction software.Above of all results in this study suggests that some mRNA,IncRNAs and circRNAs may involved the process of muscle development with different expression patterns.The identification and function analysis of Zika rabbit IncRNAs lays a foundation for further study of growth of skeletal muscle mechanism and can be reference to study IncRNA and circRNAs using rabbit as an animal model,which will further promote the study of IncRNA functions and gene regulatory mechanisms in rabbit.