苹果响应盐胁迫相关miRNA的深度测序数据集

doi:10.19788/j.issn.2096-6369.100007

农业大数据学报 ›› 2024, Vol. 6 ›› Issue (1): 14-23.doi: 10.19788/j.issn.2096-6369.100007

苹果响应盐胁迫相关miRNA的深度测序数据集

刘昭¹^,²(), 高源², 王昆², 孙思邈², 代瑛姿¹, 路翔¹^,², 田雯¹^,², 王大江²^,^*(), 冯建荣¹^,^*()

1.石河子大学农学院/特色果树栽培生理与种质资源利用兵团重点实验室，新疆石河子832000
2.中国农业科学院果树研究所/农业农村部园艺作物种质资源利用重点实验室，辽宁兴城125100

收稿日期:2023-12-23 接受日期:2024-01-26 出版日期:2024-03-26 发布日期:2024-04-08
通讯作者: 冯建荣，E-mail:fjr_agr@shzu.edu.cn；王大江，E-mail:dajiang0101@163.com。
作者简介:刘昭，E-mail:Lz__0427@163.com。
基金资助:
2023年新疆建设兵团研究生科研创新项目;中国农业科学院创新工程项目(CAAS-ASTIP-2021-RIP-02)

Deep Sequencing Dataset of miRNAs in Response to Salt Stress in Apples

LIU Zhao¹^,²(), GAO Yuan², WANG Kun², SUN SiMiao², DAI YingZi¹, LU Xiang¹^,², TIAN Wen¹^,², WANG DaJiang²^,^*(), FENG JianRong¹^,^*()

1. College of Agriculture, Shihezi University, Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi 832000, Xinjiang, China
2. Research Institute of Pomology, Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Xingcheng 125100, Liaoning, China

Received:2023-12-23 Accepted:2024-01-26 Online:2024-03-26 Published:2024-04-08

摘要/Abstract

摘要：

土壤盐渍化已成为限制农作物产量与质量的重要因素之一，影响着全世界范围内的农作物产量。苹果作为一种重要的水果作物，盐胁迫的危害及耐盐砧木的缺乏已成为威胁现代苹果产业健康可持续发展的重要问题。因此，研究苹果对盐胁迫的反应和适应具有重要的现实意义和紧迫性。本研究分别以0%、0.2%和0.6% NaCl处理0、4、8和12天后的珠美海棠实生苗为试验材料，从叶片及根系中提取总RNA，构建RNA-seq文库，共鉴定获得575个miRNA，包括315个已知mdm-miRNA和260个新miRNA。此外，Differential Expression（DE） miRNA对盐胁迫反应具有组织特异性表达模式。同时提供珠美海棠miRNA深度测序的数据集，结合生物信息学方法对原始数据质量控制，获得高质量序列并利用BLAST软件将预测靶基因序列与NR、Swiss-Prot、Pfam等数据库比对，获得响应盐胁迫相关基因的注释信息。GO分析表明与盐胁迫有关miRNA及靶基因主要参与生物过程中对刺激的反应。本研究为珠美海棠的利用提供理论数据基础，并为耐盐砧木的选育提供有力支持。

数据摘要：

项目	描述
数据库（集）名称	苹果响应盐胁迫相关miRNA的深度测序数据集
所属学科	农学，生物学
研究主题	苹果盐处理的RNA-seq数据
数据时间范围	2017年—2023年
数据类型与技术格式	.FASTQ,.STAT
数据库（集）组成	本数据集由.FASTQ,.STAT文件格式和4个表格数据组成，主要包括珠美海棠苹果叶片及根系的miRNA测序结果和注释到的耐盐靶基因数据
数据量	9.19GB
主要数据指标	数据质量控制、已知miRNA和新miRNA预测、miRNA前体结构、靶基因预测、靶基因注释
数据可用性	DOI: 10.57760/sciencedb.agriculture.00097 CSTR: 17058.11.sciencedb.agriculture.00097 数据服务系统网址： https://www.scidb.cn/s/iqmQfi
经费支持	2023年新疆建设兵团研究生科研创新项目；中国农业科学院创新工程项目（CAAS-ASTIP-2021-RIP-02）

关键词: 苹果, 盐胁迫, miRNA, 深度测序, 生物信息学

Abstract:

Soil salinization has become an important factor limiting crop yield and quality, affecting crop yields worldwide. As an important fruit crop, the harm of salt stress and the lack of salt tolerant rootstocks have become important issues threatening the healthy and sustainable development of the modern apple industry. Therefore, studying the response and adaptation of apple trees to salt stress is of great practical significance and urgency. In this study, total RNA was extracted from the leaves and roots of Malus zumi (Mats.) Rehd. seedlings were treated with 0, 0.2% and 0.6% NaCl after 0, 4, 8 and 12 days, and RNA-seq libraries were constructed. A total of 575 miRNAs were identified, including 315 known mdm-miRNAs and 260 new miRNAs. In addition, differentially expressed (DE) miRNAs exhibited tissue-specific expression patterns in response to salt stress. At the same time, a data set for deep sequencing of miRNA in Malus zumi (Mats.) Rehd was provided, and bioinformatics methods were used to control the quality of the original data. High quality sequences were obtained, and BLAST software was used to compare the predicted target gene sequences with NR, Swiss Prot, Pfam and other databases to obtain annotation information of salt tolerance related genes. GO analysis shows that miRNAs and target genes related to salt stress are mainly involved in the response to stimuli in biological processes. This will provide theoretical data basis for the utilization of Malus zumi (Mats.) Rehd and favorable support for the breeding of salt tolerant rootstocks.

Data Summary:

Item	Description
Dataset name	Deep Sequencing Dataset of miRNAs in Response to Salt Stress in Apples
Specific subject area	Agronomy, biology
Research Topic	RNA-seq data from apple with NaCl treatment
Time range	2017-2023
Data types and technical formats	.FASTQ,.STAT
Dataset structure	This dataset is composed of.FASTQ and.STAT file format and 4 table data, mainly including miRNA sequencing results of leaves and roots of Malus zumi (Mats.) and annotated salt tolerance target gene data
Volume of dataset	9.19GB
Key index in dataset	Data quality control, prediction of known and new miRNAs, miRNA precursor structures, prediction of target genes, and annotation of target genes
Data accessibility	DOI: 10.57760/sciencedb.agriculture.00097 CSTR: 17058.11.sciencedb.agriculture.00097 https://www.scidb.cn/s/iqmQfi
Financial support	2023 Xinjiang Construction Corps graduate research and innovation project; The Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2021-RIP-02)

Key words: apple, salt stress, miRNA, deep sequencing, bioinformatics

刘昭, 高源, 王昆, 孙思邈, 代瑛姿, 路翔, 田雯, 王大江, 冯建荣. 苹果响应盐胁迫相关miRNA的深度测序数据集[J]. 农业大数据学报, 2024, 6(1): 14-23.

LIU Zhao, GAO Yuan, WANG Kun, SUN SiMiao, DAI YingZi, LU Xiang, TIAN Wen, WANG DaJiang, FENG JianRong. Deep Sequencing Dataset of miRNAs in Response to Salt Stress in Apples[J]. Journal of Agricultural Big Data, 2024, 6(1): 14-23.

图/表 8

图1

表1

测序数据评估"

样品处理 Sample processing	样品名称 Sample name	原始序列 Raw_reads	高质量序列 Clean_reads	质量值 Q30(%)	GC含量 GC(%)
NaCl处理0d叶片	S01	13,846,490	13,803,489	99.27	44.59
	S02	20,053,068	19,987,801	99.18	44.33
	S03	13,248,886	13,214,960	99.21	43.76
NaCl处理0d根系	S04	15,468,076	15,424,018	99.14	46.47
	S05	13,351,285	13,302,893	99.35	47.21
	S06	10,676,243	10,649,229	99.20	45.67
0.2% NaCl处理4d叶片	S07	12,617,241	12,582,648	99.11	43.12
	S08	15,153,199	15,132,214	99.28	45.30
	S09	16,511,487	16,477,016	99.22	42.71
0.2% NaCl处理4d根系	S10	17,667,023	17,611,616	99.15	45.62
	S11	17,817,063	17,765,179	99.26	45.92
	S12	18,629,839	18,579,325	99.28	44.25
0.6% NaCl处理4d叶片	S13	19,289,050	19,245,145	99.22	42.42
	S14	15,140,835	15,104,430	99.25	42.73
	S15	11,550,839	11,525,892	99.21	42.65
0.6% NaCl处理4d根系	S16	16,644,254	16,611,292	99.09	48.27
	S17	20,776,915	20,721,649	99.06	48.36
	S18	14,846,340	14,790,580	99.09	49.37
0.2% NaCl处理8d叶片	S19	17,402,258	17,376,093	99.25	41.67
	S20	13,155,001	13,123,833	99.24	42.70
	S21	14,710,684	14,688,830	99.25	42.16
0.2% NaCl处理8d根系	S22	11,453,041	11,420,547	99.15	45.50
	S23	9,335,753	9,305,655	99.29	47.38
	S24	10,551,578	10,515,517	99.13	47.30
0.6% NaCl处理8d叶片	S25	11,239,238	11,208,905	99.26	42.80
	S26	15,990,661	15,940,683	99.16	42.96
	S27	9,393,863	9,375,936	99.20	41.92
0.6% NaCl处理8d根系	S28	12,091,968	12,050,134	99.10	45.49
	S29	14,053,417	14,011,022	99.34	44.95
	S30	12,830,498	12,770,615	99.15	48.28
0.2% NaCl处理12d叶片	S31	17,753,496	17,723,847	99.06	44.14
	S32	17,291,050	17,271,228	99.26	41.02
	S33	12,277,158	12,239,966	99.18	43.46
0.2% NaCl处理12d根系	S34	10,725,382	10,686,784	98.99	45.53
	S35	12,884,009	12,858,176	99.09	46.14
	S36	18,365,765	18,289,799	99.09	46.03
0.6% NaCl处理12d叶片	S37	20,567,162	20,521,482	99.18	43.67
	S38	18,505,328	18,469,101	99.21	43.66
	S39	20,211,075	20,171,756	99.16	43.69
0.6% NaCl处理12d根系	S40	23,937,701	23,858,507	99.22	45.79
	S41	20,858,808	20,809,845	99.16	46.82
	S42	21,005,855	20,936,321	99.24	45.92

表1

图2

图3

表2

表3

表4

图4

参考文献 22

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种类 Types	全部miRNA数量 Total number of miRNAs	靶向miRNA数量 Number of targeted miRNAs	靶基因数量 Number of target genes
Known miRNA	315	315	4,459
Novel miRNA	260	242	1,714
Total	575	557	5,812

靶基因注释数据库 Anno Database	注释到的数量 Annotated Number	300≤长度<1000 300≤length<1000	长度≥1000 Length≥1000
COG_Annotation	2,363	184	2,173
GO_Annotation	3,525	462	3,042
KEGG_Annotation	2,229	267	1,951
KOG_Annotation	3,390	386	2,982
Pfam_Annotation	4,899	551	4,332
Swissprot_Annotation	4,653	578	4,053
eggNOG_Annotation	5,497	722	4,748
nr_Annotation	5,690	813	4,847
All_Annotated	5,692	814	4,848

响应盐胁迫靶基因 Target genes in response to salt stress	数目 Number
钠/氢反转运蛋白（Na⁺/H⁺Antiporter, NHX）	5
丝氨酸/苏氨酸类蛋白激酶（Mitogen-activated protein kinase, MAPK）	8
钙依赖蛋白激酶（Calcium-dependent protein kinase, CDPK）	2
钙调磷酸酶B样蛋白（Calcineurin B-like proteins, CBLs）	2
类钙调素蛋白（Calmodulin-like proteins, CML）	5
L-抗坏血酸过氧化物酶（Ascorbate peroxidase, APX）	4
富含亮氨酸重复序列延伸蛋白（Leucine-rich repeat extensin, LRX）	2
快速碱化因子（Rapid alkalinization factor, RALF）	1
类受体蛋白激酶（FERONIA, FER）	6
WRKY转录因子	21
MYB转录因子	58
NAC转录因子	26
bHLH转录因子	23
AP2/ERF转录因子	1
bZIP转录因子	8
DREB转录因子	3
zinc finger转录因子	38

苹果响应盐胁迫相关miRNA的深度测序数据集

Deep Sequencing Dataset of miRNAs in Response to Salt Stress in Apples

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