Transcriptome analysis of leaves of wild Portulaca oleracea L. based on Iso-Seq technology

doi:10.3969/j.issn.1004-1524.2023.01.08

Acta Agriculturae Zhejiangensis ›› 2023, Vol. 35 ›› Issue (1): 67-78.DOI: 10.3969/j.issn.1004-1524.2023.01.08

• Horticultural Science • Previous Articles Next Articles

Transcriptome analysis of leaves of wild Portulaca oleracea L. based on Iso-Seq technology

YE Meirong(), HUANG Shoucheng, WANG Xiaopeng, LIU Airong, CUI Feng, KANG Jian

College of Life and Health Sciences, Anhui Science and Technology University, Fengyan 233100, Anhui,China

Received:2022-09-24 Online:2023-01-25 Published:2023-02-21

Abstract

Abstract:

The transcriptome of wild Portulaca oleracea’s leaves (leaves of three treatments: control, drought stress and low temperature stress) was sequenced and analyzed by Iso-Seq technology. The results showed that 641 732 polymerase reads were generated from the transcriptome of P. oleracea’s leaves. 26 758 071 subreads and 44 Gb total bases were obtained by quality control methods. 442 760 consensus sequences were generated by using CCS software. 391 258 full-length reads and 301 412 full-length non-chimeric reads were generated based on Smrtlink software. 103 298 transcripts were obtained from these consensus sequences by removing redundancy, and 39 717 unigenes were generated from these transcripts by removing redundancy. 40 952 LncRNAs and 38 419 CDS sequences were predicted from the unigenes. Unigenes were aligned to the sequences of public databases, including UniProt, Pfam, GO, KEGG, eggNOG, pathway and NR databases, in which 36 381 unigenes were annotated, and 25 898 (simple sequence repeats) SSR loci were detected in the unigenes. The differentially expressed genes (DEGs) among different treatment groups were screened by using DESeq 2.16 194(Up: 2 874, Down: 13 320), 16 093 (Up: 6 365, Down: 9 728) and 25 498 (Up: 15 163, Down: 10 335) DEGs were obtained in C vs DS, C vs LTS, and DS vs LTS, respectively. This study could provide reference for gene research and SSR development of P. oleracea.

Key words: Portulaca oleracea L., transcriptome, Iso-Seq technology

CLC Number:

YE Meirong, HUANG Shoucheng, WANG Xiaopeng, LIU Airong, CUI Feng, KANG Jian. Transcriptome analysis of leaves of wild Portulaca oleracea L. based on Iso-Seq technology[J]. Acta Agriculturae Zhejiangensis, 2023, 35(1): 67-78.

Figures/Tables 15

Table 1 The statistics of primary transcripts

类型 Type	片段数量 Number of reads/bp
一致序列数目 Number of consensus reads	442 760
含有5'引物的插入片段的条数 Number of 5' primer reads	430 646
含有3'引物的插入片段的条数 Number of 3' primer reads	430 907
含有poly-A的插入片段的条数 Number of poly-A reads	403 679
过滤掉的短序列数目 Number of filtered short reads	27
非全长的插入片段数目 Number of non-full-length reads	51 475
全长的插入片段数目 Number of full-length reads	391 258
全长并去除嵌合体的插入片段数目 Number of full-length non-chimeric reads	301 412
全长非嵌合序列平均长度 Mean full-length non-chimeric reads	1 577

Fig.1 Length distribution of unigene

Fig.2 All LncRNA length distribution

Fig.3 Length distribution of CDS

Fig.4 The statistical of the Unigene annotation

Fig.5 GO function annotation

Fig.6 KEGG function annotation

Fig.7 COG function annotation

Fig.8 Nr annotation

Fig.9 The E-value of Nr annotation

Fig.10 Identity distribution of Nr annotation

Fig.11 Pfam domain annotation

Fig.12 Number of SSR types

Fig.13 Distribution of differentially expressed genes A, C vs DS Volcano; B, C vs LTS Volcano; C, 15 DSvsLTS Volcano; D, Venn diagram of DEGs in different comparisons.

Fig.14 GO classification of DEGs in C vs DS (A), C vs TS (B), DS vs LTS (C)

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Transcriptome analysis of leaves of wild Portulaca oleracea L. based on Iso-Seq technology

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