Biotechnology Bulletin ›› 2021, Vol. 37 ›› Issue (8): 131-140.doi: 10.13560/j.cnki.biotech.bull.1985.2021-0191
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SHANG Xiao-yao(), ZHOU Ling-fang, YIN Qian-qian, CHAO Yue-hui()
Received:
2021-02-18
Online:
2021-08-26
Published:
2021-09-10
Contact:
CHAO Yue-hui
E-mail:sxy997987281@163.com;chaoyuehui@bjfu.edu.cn
SHANG Xiao-yao, ZHOU Ling-fang, YIN Qian-qian, CHAO Yue-hui. Sequencing and Analysis of Full-length Transcriptome from Medicago truncatula[J]. Biotechnology Bulletin, 2021, 37(8): 131-140.
类别 Category | 数目 Amount | 最小长度 Min length/bp | 最大长度 Max length/bp | 平均长度 Mean length/bp | N50长度 N50 length/bp |
---|---|---|---|---|---|
Subread | 7 728 183 | 51 | 73 164 | 1 524 | 2 051 |
CCS | 659 220 | 200 | 17 791 | 2 257 | 2 757 |
FLNC | 509 014 | 200 | 17 128 | 2 047 | 2 440 |
ICE consensus | 243 832 | 200 | 17 128 | 2 305 | 3 367 |
Polished consensus | 243 676 | 166 | 17 128 | 2 321 | 3 380 |
Corrected consensus | 236 243 | 260 | 17 954 | 2 425 | 3 496 |
Table 1 Statistics of sequencing data by SMRT
类别 Category | 数目 Amount | 最小长度 Min length/bp | 最大长度 Max length/bp | 平均长度 Mean length/bp | N50长度 N50 length/bp |
---|---|---|---|---|---|
Subread | 7 728 183 | 51 | 73 164 | 1 524 | 2 051 |
CCS | 659 220 | 200 | 17 791 | 2 257 | 2 757 |
FLNC | 509 014 | 200 | 17 128 | 2 047 | 2 440 |
ICE consensus | 243 832 | 200 | 17 128 | 2 305 | 3 367 |
Polished consensus | 243 676 | 166 | 17 128 | 2 321 | 3 380 |
Corrected consensus | 236 243 | 260 | 17 954 | 2 425 | 3 496 |
数据库 Databases | 新基因注释数量 Number of functional annotated novel genes |
---|---|
NR | 5 183 |
SwissProt | 2 370 |
KEGG | 4 532 |
KOG | 1 884 |
GO | 1 717 |
NT | 6 916 |
PFAM | 1 717 |
总计 Total | 7 209 |
未注释 Unannotated ones | 227 |
Table 2 Functional annotations of novel genes
数据库 Databases | 新基因注释数量 Number of functional annotated novel genes |
---|---|
NR | 5 183 |
SwissProt | 2 370 |
KEGG | 4 532 |
KOG | 1 884 |
GO | 1 717 |
NT | 6 916 |
PFAM | 1 717 |
总计 Total | 7 209 |
未注释 Unannotated ones | 227 |
序列来源 Sequence origin | 编码区数量 Number of CDS | 编码区平均长度 Mean CDS length/bp | 完整编码区数量 Number of complete CDS | 3'非编码区数量 Number of 3'-UTR | 5'非编码区数量 Number of 5'-UTR |
---|---|---|---|---|---|
SMRT | 36 235 | 1 027.03 | 13 451 | 1 990 | 11 071 |
R108 | 61 020 | 874.54 | 16 313 | 3 895 | 4 928 |
Table 3 CDS and UTR identification
序列来源 Sequence origin | 编码区数量 Number of CDS | 编码区平均长度 Mean CDS length/bp | 完整编码区数量 Number of complete CDS | 3'非编码区数量 Number of 3'-UTR | 5'非编码区数量 Number of 5'-UTR |
---|---|---|---|---|---|
SMRT | 36 235 | 1 027.03 | 13 451 | 1 990 | 11 071 |
R108 | 61 020 | 874.54 | 16 313 | 3 895 | 4 928 |
Fig.5 Distribution of exons in transcripts Pac-Bio:SMRT transcripts. R108:Transcripts from M. truncatula R108 reference genome.A17:Transcripts from M. truncatula A17 reference genome
Fig.6 Numbers and types of AS events SE:Skipped exon. MX:mutually exclusive exon. A5:Alternative 5' splice site. A3:Alternative 3' splice site. RI:Retained intron. AF:First exon is alternative splice. AL:Last exon is alternative splice
转录本数目 Number of transcript | SMRT测序 SMRT sequence | 参考基因组 Reference genome |
---|---|---|
1 | 11 730 | 52 332 |
2 | 4 713 | 2 308 |
3 | 2 660 | 617 |
4 | 1 614 | 246 |
5 | 965 | 96 |
6 | 618 | 58 |
7 | 415 | 21 |
8 | 334 | 10 |
9 | 216 | 8 |
10 | 147 | 5 |
>10 | 514 | 5 |
Table 4 Number of transcripts in SMRT sequence and reference genomes
转录本数目 Number of transcript | SMRT测序 SMRT sequence | 参考基因组 Reference genome |
---|---|---|
1 | 11 730 | 52 332 |
2 | 4 713 | 2 308 |
3 | 2 660 | 617 |
4 | 1 614 | 246 |
5 | 965 | 96 |
6 | 618 | 58 |
7 | 415 | 21 |
8 | 334 | 10 |
9 | 216 | 8 |
10 | 147 | 5 |
>10 | 514 | 5 |
Fig.7 Identification of lncRNA A:Venn diagram of lncRNAs predicted by CPC,CNCI,PLEK and Pfam methods.B:Proportions of 4 types of lncRNA identified by SMRT
Fig. 9 Analysis of poly(A)sites A:Distribution of the number of poly(A)sites per gene. B:Nucleotide composition around poly(A)cleavage sites. C:MEME analysis of repeated sequence in the upstream of the poly(A)site. D:MEME analysis of repeated sequence in the downstream of the poly(A)site
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