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)

References 14

[1]	刘学军, 瞿锡垚, 张礼. 保留非全长读段的ISO-seq数据转录组表达分析[J]. 数据采集与处理, 2019, 34(4): 594-604.
	LIU X J, QU X Y, ZHANG L. Transcriptome expression analysis of ISO-seq data with non-full-length reads reserved[J]. Journal of Data Acquisition and Processing, 2019, 34(4): 594-604. (in Chinese with English abstract)
[2]	任毅鹏, 张佳庆, 孙瑜, 等. 基于PacBio平台的全长转录组测序[J]. 科学通报, 2016, 61(11): 1250-1254.
	REN Y P, ZHANG J Q, SUN Y, et al. Full-length transcriptome sequencing on Pac Bio platform[J]. Chinese Science Bulletin, 2016, 61(11): 1250-1254. (in Chinese with English abstract)
[3]	赵陆滟, 曹绍玉, 龙云树, 等. 全长转录组测序在植物中的应用研究进展[J]. 植物遗传资源学报, 2019, 20(6): 1390-1398.
	ZHAO L Y, CAO S Y, LONG Y S, et al. Applications and research progresses of full-length transcriptome sequencing in plants[J]. Journal of Plant Genetic Resources, 2019, 20(6): 1390-1398. (in Chinese with English abstract)
[4]	KUANG X, SUN S, WEI J, et al. Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis[J]. BMC Plant Biology, 2019, 19(1): 210. DOI URL
[5]	吉占和, 陈心启, 罗毅波, 等. 中国植物志[M]. 北京: 科学出版社, 19997.
[6]	BEHRAVAN J, MOSAFA F, SOUDMAND N, et al. Protective effects of aqueous and ethanolic extracts of Portulaca oleracea L. aerial parts on H₂O₂-induced DNA damage in lymphocytes by comet assay[J]. Journal of Acupuncture and Meridian Studies, 2011, 4(3): 193-197. DOI URL
[7]	UDDIN M K, JURAIMI A S, HOSSAIN M S, et al. Purslane weed (Portulaca oleracea): a prospective plant source of nutrition, Omega-3 fatty acid, and antioxidant attributes[J]. The Scientific World Journal, 2014, 2014: 951019.
[8]	ZHOU Y X, XIN H L, RAHMAN K, et al. Portulaca oleraceaL.: a review of phytochemistry and pharmacological effects[J]. BioMed Research International, 2015, 2015: 1-11.
[9]	刘翠艳, 陈四玉, 孙桃桃, 等. 马齿苋-益生菌联用对热毒证小鼠腹泻的预防效果[J]. 浙江农业学报, 2018, 30(2): 211-219. DOI
	LIU C Y, CHEN S Y, SUN T T, et al. Preventive effect of purslane combined with probiotics on heat-toxin syndrome diarrhea mice[J]. Acta Agriculturae Zhejiangensis, 2018, 30(2): 211-219. (in Chinese with English abstract) DOI
[10]	李海涛, 葛翎, 段国梅, 等. 马齿苋的化学成分及药理活性研究进展[J]. 中国野生植物资源, 2020, 39(6): 43-47.
	LI H T, GE L, DUAN G M, et al. Research progress on chemical constituents and pharmacological activities of Portulaca oleracea L[J]. Chinese Wild Plant Resources, 2020, 39(6): 43-47. (in Chinese with English abstract)
[11]	YANG Y, CHEN J, LIU Q, et al. Comparative proteomic analysis of the thermotolerant plant Portulaca oleracea acclimation to combined high temperature and humidity stress[J]. Journal of Proteome Research, 2012, 11(7): 3605-3623. DOI URL
[12]	胡水清青, 杜红梅. NaCl处理对马齿苋植株生长的影响[J]. 上海交通大学学报(农业科学版), 2018, 36(5): 67-72.
	HU S, DU H M. The effects of NaCl treatment on growth of purslane (Portulaca oleracea)[J]. Journal of Shanghai Jiao Tong University (Agricultural Science), 2018, 36(5): 67-72. (in Chinese with English abstract)
[13]	张边江, 唐宁, 华春, 等. 海水胁迫下马齿苋光合及抗氧化生理特性研究[J]. 草地学报, 2015, 23(4): 878-882. DOI
	ZHANG B J, TANG N, HUA C, et al. Effects of seawater stress on photosynthetic and antioxidant characteristics in Portulaca oleracea[J]. Acta Agrestia Sinica, 2015, 23(4): 878-882. (in Chinese with English abstract)
[14]	王竹承, 左丽丽. 干旱胁迫对马齿苋种子萌发和幼苗生长的影响[J]. 沧州师范学院学报, 2019, 35(1): 66-73.
	WANG Z C, ZUO L L. Effects of drought stress on seed germination and seedling growth of purslane[J]. Journal of Cangzhou Normal University, 2019, 35(1): 66-73. (in Chinese with English abstract)

[1]	XIONG Xingwei, WANG Yiqin, TIAN Huaizhi, ZHANG Suqin, GENG Guangdong. Molecular mechanisms of chlorophyll-reduced cotyledon based on transcriptome sequencing in pumpkin [J]. Acta Agriculturae Zhejiangensis, 2023, 35(1): 90-102.
[2]	GU Xianbin, LU Linghong, SONG Genhua, XIAO Jinping, ZHANG Huiqin. Regulation effect of melatonin pretreatment on waterlogging tolerance in peach seedling [J]. Acta Agriculturae Zhejiangensis, 2022, 34(9): 1911-1924.
[3]	WANG Siliang, SHAO Yue, YAN Chengjin. Transcriptome analysis of Spodoptera furgiperda during corn-wheat host alternation [J]. Acta Agriculturae Zhejiangensis, 2022, 34(6): 1236-1247.
[4]	LIU Chen, XU Haobo, SI Yuyang, LI Yapeng, GUO Yuting, DU Changxia. Research progress on regulation mechanism of plant response to salt stress based on transcriptomics [J]. Acta Agriculturae Zhejiangensis, 2022, 34(4): 870-878.
[5]	WANG Qiankun, ZHANG Xiaohui, PANG Youzhi, QI Yanxia, LEI Ying, BAI Junyan, HU Yunqi, ZHAO Yiwei, YUAN Zhiwen, WANG Tao. Screening of genes related to auto-sexing on feather color based on RNA-seq technology [J]. Acta Agriculturae Zhejiangensis, 2022, 34(3): 498-506.
[6]	LAN Guoxiang, JIN Siqi, LI Xingrun, LIU Xiyu, LI Guomei, DONG Xinxing. Screening and functional analysis of differentially expressed genes in breast muscle transcriptome between Plateau raindrop pigeon and Janssen pigeon [J]. Acta Agriculturae Zhejiangensis, 2022, 34(3): 507-516.
[7]	YANG Xinxia, TANG Mansheng, ZHANG Bin. Identification of soybean PP2C family genes and transcriptome analysis in response to salt stress [J]. Acta Agriculturae Zhejiangensis, 2022, 34(2): 207-220.
[8]	LIANG Qianrong, ZHENG Tianlun, CHEN Xiaoming, ZHU Ningyu, ZHENG Xiaoye, HE Runzhen, CAO Feifei, XUE Huili, DING Xueyan. Effects of feeding with maggot protein added dietaries on immune and metabolic responses in liver and serum of soft-shelled turtles Pelodiscus sinensis [J]. Acta Agriculturae Zhejiangensis, 2022, 34(10): 2172-2181.
[9]	YIN Minghua, BAI Li, CHEN Shumin, CHENG Jiahui, FENG Liwen. Transcriptome analysis of virus-free microtubers of Dioscorea polystachya Turczaninow. cv. Guangfeng Qianjin and Dioscorea polystachya Turczaninow. cv. Tiegun [J]. Acta Agriculturae Zhejiangensis, 2022, 34(10): 2209-2219.
[10]	MA Jie, QU Wen, CHEN Chunyan, WANG Lei, MA Jun, LIU Zhenshan, MA Wei, ZHOU Ping, HE Yuankuan, SUN Bo. Development of SSR markers based on transcriptome sequencing and genetic diversity analysis of Nainaiqingcai leaf mustard [J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1640-1649.
[11]	HUANG Changbing, CHENG Peilei, YANG Shaozong, ZHANG Huanchao, JIANG Zhengzhi, JIN Limin. Transcriptome analysis of Hemerocallis fulva under low temperature stress [J]. Acta Agriculturae Zhejiangensis, 2021, 33(8): 1445-1460.
[12]	JIANG Zhifang, HAN Yidie, LOU Panpan, GUO Hong, FENG Shangguo, SHEN Chenjia, WANG Huizhong1. Identification and expression analysis of cytochrome P450 family genes from Physalis angulata L. [J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2009-2016.
[13]	FENG Shangle, LI Xuenan, CHEN Yige, LIU Ruiqi, BAI Zhiyi, LI Wenjuan. Screening and expression of cyclins gene in Hyriopsis cumingii [J]. Acta Agriculturae Zhejiangensis, 2021, 33(11): 2041-2050.
[14]	YIN Minghua, CAO Qing, CHEN Hong, DENG Siyu, DENG Yanmei. Transcriptome analysis of red bud taro and green stem taro in Yanshan, Jiangxi Province [J]. , 2020, 32(9): 1533-1543.
[15]	LIU Xinyu, TIAN Jie. Analysis of simple sequence repeats in transcriptome of garlic (Allium sativum L.) and development of molecular markers [J]. , 2020, 32(9): 1615-1625.

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

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 15

References 14

Related Articles 15

Recommended Articles

Metrics

Comments