Transcriptome Sequencing and Bioinformatics Analysis of Astragalus complanatus

doi:10.7668/hbnxb.20192406

Abstract

Abstract:

In order to obtain transcriptome information and functional genes expression characteristics of Astragalus complanatus,the leaves of A.complanatus were used as material,the high-throughput transcriptome sequencing and bioinformatics analysis were performed using Illumina HiSeq platform.A total of 19 280 Unigenes were assembled with total sequence length of 23 472 470 bp,of which the GC content was 42.74%,indicating a high quality of sequencing and assembly.Blast analysis showed 12 541,10 120,9 412,8 953,7 494,5 052 Unigenes got annotation in Nr,Swiss-Prot,GO,KEGG,KOG and COG databases,respectively.The annotated Unigenes of A.complanatus were mainly homologuous to leguminous plants,in particular,highly matched to the subfamily Pteriformis plant Cicer arietinum,Medicago truncatula and Abrus precatorius with a respective percentage of 31.49%,14.50% and 11.65%.Annotated Unigenes were divided into 3 GO classifications,354 KEGG metabolic pathways and 25 KOG function categories.The most abundant categories in each database were metabolic process,general function prediction only and purine metabolism,respectively.These results showed that the leaf cells of Astragalus membranaceus had active metabolism and abundant gene expression in the seedling stage.Additionally,a lot of Unigenes were annotated to the infectious disease category in KEGG database,suggesting a potential medicinal value of the plant part of Astragalus membranaceus.A total of 5 849 simple sequence repeats(SSRs)were identified by MISA software,with an occurrence frequency of 30.34%.The SSRs in the genome of Astragalus membranaceus were abundant and diversified,containing single base to six base repeats,among which the mono-nucleotide SSRs had the largest number with a frequency of 40.56%.The main types of SSR motifs involved A/T,AG/CT and AAG/CTT.

Key words: Astragalus complanatus, Transcriptome, Bioinformatics, Unigene, Molecular marker

WU Yue, CHEN Yang, WANG Xingzhe, SHAN Feibiao, ZHANG Yong, SUN Hongju. Transcriptome Sequencing and Bioinformatics Analysis of Astragalus complanatus[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(1): 42-49. doi: 10.7668/hbnxb.20192406.

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Figures/Tables 10

Tab.1 Quality analysis of sequencing data

高质量序列 Clean reads	高质量碱基/bp Clean bases	GC含量/% GC content	Q20碱基数占比/%	Q30碱基数占比/%
33 217 041	9 965 112 300	42.74	98.03	93.89

Tab.2 The statistics analysis of Astragalus complanatus transcript and Unigene

类别 Categories	转录本 Transcript	单基因簇 Unigene
序列总数目	21 565	19 280
Total sequence number
序列总长度/bp	27 333 335	23 472 470
Total sequence length
最大长度/bp	15 713	15 713
Maximum length
最小长度/bp	201	201
Minimum length
平均长度/bp	1 267	1 217
Average length
GC含量/%	40.37	40.38
GC content
N50/bp	2 079	2 094

Fig.1 The statistics analysis of annotated Unigene in Astragalus complanatus

Fig.2 Matched species distribution of Astragalus complanatus Unigene in Nr database

Fig.3 Functional classification of Astragalus complanatus Unigene in GO database
1.Extracellular region;2.Cell;3.Nucleoid;4.Membrane;5.Virion;6.Cell junction;7.Membrane-enclosed lunen;8.Protein-containing complex;9.Organelle;10.Extracellular region part;11.Organelle part;12.Virion part;13.Membrane part;14.Cell part;15.Supramolecular complex;16.Catalytic activity;17.Structural molecule activity;18.Transporter activity;19.Binding;20.Antioxidant activity;21.Protein tag;22.Cargo receptor activity;23.Protein folding chaperone;24.Translation regulator actiivty;25.Nutrient reservoir activity;26.Molecular transducer activity;27.Molecular function regulator;28.Molecular carrier activity;29.Transciption regulator activity;30.Small molecule sensor activity;31.Reproduction;32.Cell killing;33.Immune system process;34.Metabolic process;35.Cell population proliferation;36.Cellular process;37.Carbon utilization;38.Nitrogen utilization;39.Reproductive process;40.Biological adhesion;41.Signaling;42.Multicellular organismal process;43.Developmental process;44.Growth;45.Locomotion;46.Rhythmic process;47.Response to stimulus;48.Localization;49.Multi-organism process;50.Biological regulation;51.Cellular component organization or biogenesis;52.Detoxification.

Tab.3 KOG function categories of Astragalus complanatus Unigene

功能名称 Function name	注释Unigene数目 Number of annotated Unigene
一般功能预测 General function prediction only	1 551
翻译后修饰、蛋白转运 Posttranslational modification, protein turnover, chaperones	926
信号传导机制 Signal transduction mechanisms	683
翻译、核糖体结构和生物起源 Translation, ribosomal structure and biogenesis	498
未知功能 Unknown function	491
碳水化合物转运和代谢 Carbohydrate transport and metabolism	459
转录 Transcription	447
细胞内运输、分泌和囊泡运输 Intracellular trafficking, secretion, and vesicular transport	433
能量生产及转换 Energy production and conversion	363
RNA加工和修饰 RNA processing and modification	358
氨基酸转运和代谢 Amino acid transport and metabolism	342
脂类转运和代谢 Lipid transport and metabolism	304
次生代谢产物的合成、转运和代谢 Secondary metabolites biosynthesis, transport and catabolism	236
无机离子的转运和代谢 Inorganic ion transport and metabolism	210
细胞周期调控、细胞分裂、染色体分离 Cell cycle control, cell division, chromosome partitioning	176
复制、重组和修复 Replication, recombination and repair	145
细胞骨架 Cytoskeleton	145
染色体结构和动力学 Chromatin structure and dynamics	125
细胞壁/细胞膜/包膜的生物发生 Cell wall/membrane/envelope biogenesis	105
核酸转运和代谢 Nucleotide transport and metabolism	102
辅酶转运和代谢 Coenzyme transport and metabolism	98
防御机制 Defense mechanisms	67
核结构 Nuclear structure	27
细胞外结构 Extracellular structures	21
细胞活性 Cell motility	3

Fig.4 Functional classification of Astragalus complanatus Unigene in KEGG database
1.Drug resistance:antimicrobial;2.Drug resistance:antineoplastic;3.Cardiovascular disease;4.Immune disease;5.Substance dependence;6.Endocrine and metabolic disease;7.Cancer:specific types;8.Neurodegenerative disease;9.Cancer:overview;10.Infectious disease:parasitic;11.Infectious disease:bacterial;12.Infectious disease:viral;13.Human diseases;14.Sensory system;15.Development and regeneration;16.Circulatory system;17.Excretory system;18.Digestive system;19.Aging;20.Nervous system;21.Endocrine system;22.Immune system;23.Organismal systems;24.Cellular community-prokaryotes;25.Cell motility;26.Cellular community-eukaryotes;27.Cell growth and death;28.Transport and catabolism;29.Cellular processes;30.Signaling molecules and interaction;31.Membrane transport;32.Signal transduction;33.Environmental information processing;34.Replication and repair;35.Transcription;36.Folding sorting and degradation;37.Transcription;38.Genetic information processing;39.Metabolism of terpenoids and polyketides;40.Xenobiotics biodegradation and metabolism;41.Metabolism of other amino acids;42.Glycan biosynthesis and metabolism;43.Metabolism of cofactors and vitamins;44.Nucleotide metabolism;45.Energy metabolism;46.Lipid metabolism;47.Amino acid metabolism;48.Carbohydrate metabolism;49.Metabolism.

Tab.4 Top ten metabolic pathways involving Astragalus complanatus Unigene

序号 Serial number	代谢通路 Pathway	Unigene数量 Number of Unigene	通路ID Pathway ID	占比/% Percentage
1	嘌呤代谢	309	ko00230	3.45
2	淀粉和蔗糖的代谢	252	ko00500	2.81
3	核糖体	227	ko03010	2.54
4	RNA转运	224	ko03013	2.50
5	剪接体	223	ko03040	2.49
6	NF-kappa B信号通路	220	ko04064	2.46
7	植物激素信号转导	213	ko04075	2.38
8	内质网中的蛋白质加工	205	ko04141	2.29
9	内吞作用	202	ko04144	2.26
10	Toll样受体信号通路	200	ko04620	2.23

Fig.5 The statistics of SSR types and main unit in Astragalus complanatus

Tab.5 SSR analysis of Astragalus complanatus transcriptome Unigene

单元重复数 Repeats	重复数 Repeats											合计 Total
单元重复数 Repeats	单核苷酸 Mono-nucleotide	二核苷酸 Di-nucleotide		三核苷酸 Tri-nucleotide		四核苷酸 Tetra-nucleotide		五核苷酸 Penta-nucleotide		六核苷酸 Hexa-nucleotide		合计 Total
5	0		0		762		99		49		24	934
6	0		317		420		53		8		3	801
7	0		233		224		7		1		0	465
8	0		225		150		1		0		1	377
9	0		154		31		2		0		0	187
10	1 026		109		34		1		0		0	1 170
11	464		151		19		1		0		0	635
>11	882		364		34		0		0		0	1 280
合计Total	2 372		1 553		1 674		164		58		28	5 849
占比/% Percentage	40.56		26.55		28.62		2.80		0.99		0.48	100

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