The number and variability of transcripts determine the diversity and complexity of the proteins in a species.To reveal the variations in transcript abundance and the related factors in Chinese fir(Cunninghamia lanceo...The number and variability of transcripts determine the diversity and complexity of the proteins in a species.To reveal the variations in transcript abundance and the related factors in Chinese fir(Cunninghamia lanceolata),we performed second-generation sequencing(RNA-seq)and third-generation sequencing(PacBio)analyses.The forms and rates of alternative splicing in Chinese fir were studied on the basis of the obtained transcripts.Furthermore,the number of full-length transcripts(isoforms)produced by alternative splicing and the variation patterns in‘Long 15'were analyzed.The transcript diversity in Chinese fir was largely caused by six alternative splicing forms,of which intron retention was the most common(47.98%of all alternative splicing events),followed by alternative 3′splice site(24.29%).The third-generation sequencing analysis detected 61613 isoforms in‘Long 15',with each gene producing 1-10 isoforms.Only 0.06%of the genes produced more than 10 isoforms.Transcript abundance was similar among Chinese fir varieties,but 615 more transcripts were detected in‘Long 15'than in clone 1339,implying that‘Long 15'synthesized more protein types in vivo than 1339.This difference may explain why‘Long 15'grows better and is more adaptable to environmental conditions than 1339.An examination of Chinese fir clone Kai6 detected more transcripts after fertilization than following a nutrient stress treatment.Moreover,transcript polymorphism was greater after fertilization than in response to nutrient stress.This finding may be useful for improving fertilizer applications to enhance Chinese fir growth and development.Sequences and alternative splicing forms are critical for research on the Chinese fir transcriptome and the potential biological consequences of alternative splicing.展开更多
基金Supported by the Fundamental Research Funds of the Central Public Welfare Research Institutes of The Chinese Academy of Forestry(CAFYbb2017ZA001-1-2)the"14^(th)Five-year"Forest Variety Breeding Project of Zhejiang Province(2021C010010808)。
文摘The number and variability of transcripts determine the diversity and complexity of the proteins in a species.To reveal the variations in transcript abundance and the related factors in Chinese fir(Cunninghamia lanceolata),we performed second-generation sequencing(RNA-seq)and third-generation sequencing(PacBio)analyses.The forms and rates of alternative splicing in Chinese fir were studied on the basis of the obtained transcripts.Furthermore,the number of full-length transcripts(isoforms)produced by alternative splicing and the variation patterns in‘Long 15'were analyzed.The transcript diversity in Chinese fir was largely caused by six alternative splicing forms,of which intron retention was the most common(47.98%of all alternative splicing events),followed by alternative 3′splice site(24.29%).The third-generation sequencing analysis detected 61613 isoforms in‘Long 15',with each gene producing 1-10 isoforms.Only 0.06%of the genes produced more than 10 isoforms.Transcript abundance was similar among Chinese fir varieties,but 615 more transcripts were detected in‘Long 15'than in clone 1339,implying that‘Long 15'synthesized more protein types in vivo than 1339.This difference may explain why‘Long 15'grows better and is more adaptable to environmental conditions than 1339.An examination of Chinese fir clone Kai6 detected more transcripts after fertilization than following a nutrient stress treatment.Moreover,transcript polymorphism was greater after fertilization than in response to nutrient stress.This finding may be useful for improving fertilizer applications to enhance Chinese fir growth and development.Sequences and alternative splicing forms are critical for research on the Chinese fir transcriptome and the potential biological consequences of alternative splicing.
