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

Abstract

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

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.

Figures/Tables 8

Fig. 1

Table 1

Evaluation of sequencing data"

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

Table 1

Fig. 2

Fig. 3

Table 2

Table 3

Table 4

Fig. 4

References 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

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

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