Transcriptome Data Analysis of Artocarpus heterophyllus Stems and Leaves

doi:10.3969/j.issn.1000-2561.2020.07.002

Abstract

Abstract:

Artocarpus heterophyllus is an important woody plant in tropical regions withhigh economic value. This test used the normal and chlorophyll deficient mutant of A. heterophyllus seedlings as the research materials. The transcriptome of the stems and leaves was sequenced by PacBio Sequel, 95 701 isoformswerefinally found. After cluster and polish, using NR, NT, GO, KOG, KEGG, Swiss-Prot and InterPro 7 databases for functional annotation, a total of 93 367 transcripts were annotated. There were 92 187 (NR), 90 326 (NT), 74 548 (Swiss-Prot), 75 396 (KEGG), 77 022 (KOG), 81 906 (InterPro) and 65 500 (GO) transcripts annotated in the seven databases respectively. In addition, a total of 85 091 CDS and 55 608 SSR sequences were detected, 4 753 transcription factors, 1 667 transcriptional regulators and 4 710 receptor-like kinases were predicted.

Key words: Artocarpus heterophyllus, transcriptome, functional annotation

CLC Number:

S718.43

PAN Min,YU Xudong,CAI Zeping,LI Jiajia,LUO Jiajia,ZHOU Dan,CHU Wenqing,QU Qian. Transcriptome Data Analysis of Artocarpus heterophyllus Stems and Leaves[J]. Chinese Journal of Tropical Crops, 2020, 41(7): 1288-1297.

Figures/Tables 12

Fig. 1 Reads classification summary

Tab. 1 Summary of data quality control

项目 Item	总读取 Total reads	总容量 Total base/GB	最大长度 Maxlength/bp	平均长度 Meanlength/bp	N50/bp
聚合酶读取	490 303	13.58	210 091	27 691.91	49 592
Subreads	8 661 811	12.80	132 829	1 478.16	1 835
去冗余后序列	95 701	0.15	7 607	1 684	1 949

Fig. 2 Sequence length distribution A: Polymerase reads length; B: Subreads length; C: Histogram for reads of insert length; D: Histogram for isoform length.

Fig. 3 CDS length distribution and SSR size distribution A: CDS length distribution; B: SSR size distribution.

Tab. 2 Quality metrics of predicted CDS

总数量 Total number	总长度 Total length/nt	N50/nt	N90/nt	最大长度 Max length/nt	最小长度 Min length/nt	GC/%
85 091	93 949 176	1 338	621	6 240	297	46.12

Tab. 3 Summary of functional annotation result

项目 Item	总计Total	数据库Database
项目 Item	总计Total	NR	NT	Swiss-Prot	KEGG	KOG	InterPro	GO	Intersection	Overrall
数量	95 701	92 187	90 326	74 548	75 396	77 022	81 906	65 500	45 703	93 367
百分比/%	100	96.33	94.38	77.90	78.78	80.48	85.59	68.44	47.76	97.56

Fig. 4 Distribution of NR annotated species and each database Venn diagram A: Distribution of NR annotated species; B: Venn diagram

Fig. 5 Function notes A: Functional distribution of KOG annotation; B: Functional distribution of KEGG annotation; C: Functional distribution of GO annotation. In figure A, 1: Translation, ribosomal structure and biogenesis; 2: Transcription; 3: Signal transduction mechanisms; 4: Secondary metabolites biosynthesis, transport and catabolism; 5: RNA processing and modification; 6: Replication, recombination and repair; 7: Posttranslational modification, protein turnover, chaperones; 8: Nucleotide transport and metabolism; 9: Nuclear structureLipid transport and metabolism; 10: Lipid transport and metabolism; 11: Intracellular trafficking, secretion, and vesicular transport; 12: Inorganic ion transport and metabolism; 13: General function prediction only; 14: Function unknown; 15Extracellular structures; 16: Energy production and conversion; 17 Defense mechanisms; 18 Cytoskeleton; 19: Coenzyme transport and metabolism; 20: Chromatin structure and dynamics; 21: Cell wall/membrane/ envelope biogenesis; 22: Cell motility; 23 Cell cycle control, cell division, chromosome partitioning; 24: Carbohydrate transport and metabolism; 25: Amino acid transport and metabolism. In figure B, 1: Transport and catabolism; 2: Signal transduction; 3: Membrane transport; 4: Translation; 5: Folding, sorting and degradation; 6: Transcription; 7: Replication and repair; 8: Global and overview maps; 9: Carbohydrate metabolism; 10: Amino acid metabolism; 11: Lipid metabolism; 12: Energy metabolism; 13: Metabolism of cofactors and vitamins; 14: Biosynthesis of other secondary metabolites; 15: Nucleotide metabolism; 16: Metabolism of other amino acids; 17: Glycan biosynthesis and metabolism; 18: Metabolism of terpenoids and polyketides; 19: Environmental adaptation; 20: Digestive system. In figure C, 1: Cellular process; 2: Metabolic process; 3: Biological regulation; 4:Regulation of biological process; 5: Response to stimulus; 6: Localization; 7: Cellular component organization or biogenesis; 8: Signaling; 9: Multicellular organismal process; 10: Developmental process; 11: Reproduction; 12:Reproductive process; 13: Negative regulation of biological process; 14: Multi- organism process; 15: Positive regulation of biological process; 16: Growth; 17: Immune system process; 18: Rrhythmic process; 19: Cell proliferation; 20: Carbon utilization; 21: Detoxification; 22: Biological adhesion; 23: Nitrogen utilization; 24: Locomotion; 25: Cell; 26: Cell part; 27: Membrane; 28: Membrane part; 29: Organelle; 30: Macromolecular complex; 31: Organelle part; 32: Membrane-enclosed lumen; 33: Extracellular region; 34: Virion; 35: Virion part; 36: Supramolecular complex; 37: Cell junction; 38: Symplast; 39: Extracellular region part; 40: Nucleoid; 41: Binding; 42: Catalytic activity; 43: Transporter activity; 44: Transcription regulator activity; 45: Structural molecule activity; 46: Molecular function regulator; 47: Signal transducer activity; 48: Antioxidant activity; 49: Molecular transducer activity; 50: Nutrient reservoir activity; 51: Molecular carrier activity; 52: Protein tag; 53: Translation regulator activity.

Fig. 6 Transcription factor family classification

Fig. 7 Transcriptional regulator family classification

Tab. 4 Summary of transcription factors transcriptional regulators and receptor-like kinases

项目Item	总序列 Total isforms	转录因子 Transcription factors	转录调控子 Transcriptional regulators	受体激酶 Receptor-like kinases
数量	95 701	4 753	1 667	4 710
百分比/%		4.97	1.74	4.92

Fig. 8 Receptor kinase family classification A: Receptor kinase family classification; B: LRR-RLK family classification; C: RLCK family classification.

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