Transcriptome Analysis of Primary Stem of Chlorophyll Deficient Mutants from Artocarpus heterophyllus

doi:10.3969/j.issn.1000-2561.2020.08.002

Abstract

Abstract:

To explore the influence of chlorophyll synthesis deficiency on the primary stem development of Artocarpus heterophyllus, the transcriptome of the primary stem of a chlorophyll deficient mutant (CDM) of A. heterophyllus was analyzed. After assembly by de novo, 295 869 Unigenes were obtained. NR, NT, Swissprot, KEGG, KOG, Pfam and GO databases were used for sequence alignment. A total of 174 291 Unigenes were annotated. After filtering the low abundance genes, 22 988 differentially expressed genes were selected. Compared with the control check (CK), there were 379 genes up-regulated in CDM and 22 609 genes down-regulated. GO classification results showed that 3712 genes were annotated and classified into three categories: molecular function, cellular component and biological process, with a total of 48 functional groups. In addition, 2080 Unigenes were involved in 19 KEGG pathways, 30 of which were involved in flavonoids biosynthesis pathways. Through transcriptome sequencing, this paper analyzed the effect of chlorophyll synthesis deficiency on the primary stem development of A. heterophyllus, which would provide data foundation for the study on the stem development of woody plants.

Key words: Artocarpus heterophyllus, chlorophyll deficient mutant, primary stem, transcriptome analysis

CLC Number:

S718.43

ZHENG Liting,YU Xudong,CAI Zeping,LUO Jiajia,WU Fanhua,DONG Junna,CAO Peina. Transcriptome Analysis of Primary Stem of Chlorophyll Deficient Mutants from Artocarpus heterophyllus[J]. Chinese Journal of Tropical Crops, 2020, 41(8): 1513-1221.

Figures/Tables 9

Fig. 1 Stem internode phenotypic characters of normal seedlings and chlorophyll deficient mutants of A. heterophyllus CK: Normal A. heterophyllus; CDM: Chlorophyll deficient mutant of A. heterophyllus; Above the dotted line is primary stem (CK is light green, CDM is white); The scale is 10 cm.

Tab. 1 RNA-Seq dates from primary stem tissues of A. heterophyllus

样品 Sample	原始数据 Total reads/M	过滤后数据 Clean reads/M	转录本 Transcripts	Q20质量值 Q20 quality value/%	Q30质量值 Q30 quality value/%	GC含量 GC content/%	N50值 N50 value/bp	数据对比效率 Clean read ratio/%
CK1	72.28	69.29	212 772	97.48	89.30	38.89	1 353	95.86
CK2	64.08	60.77	231 308	97.25	88.68	39.17	1 218	94.83
CDM1	72.69	69.95	64 907	97.50	89.51	42.24	1 933	96.24
CDM2	70.18	67.45	74 169	97.55	89.63	41.91	1 961	96.11
CDM3	70.18	67.58	79 299	97.48	89.36	41.72	2 039	96.29

Fig. 2 Sample clustering, correlation and principal component analysis A: Cluster the samples according to the gene expression level; B: Sample correlation analysis; C: Principal component analysis of samples.

Tab. 2 Summary for the BLAST results of A. heterophyllus primary stem transcriptome against seven databases

注释的数据库 Annotated database	注释的基因数量 Annotated gene number	基因比例 Gene percentage/%
NR	152 036	51.39
NT	156 922	53.04
Swissprot	111 271	37.61
KEGG	119 331	40.33
KOG	119 737	40.47
Pfam	110 505	37.35
GO	101 591	34.34
总注释基因	174 291	58.91

Fig. 3 Statistics and analysis of DEGs in the primary stem of A. heterophyllus A: Number of genes with different expression levels in CK and CDM; B: Volcano map of DEGs between CK and CDM; C: Venn map of DEGs in each part; D: Comparison of DEGs length; E: Gene cluster tree and its module; F: Heat map and feature vector of DEGs in each sample;Ⅰ: Unique gene in CK; Ⅱ: Common genes of CK and CDM are down-regulated in CDM; Ⅲ: Common genes of CK and CDM are up-regulated in CDM; Ⅳ: Unique gene in CDM.

Fig. 4 GO function classification of DEGs

Fig. 5 KEGG functional annotation of DEGs

Fig. 6 GO enrichment of DEGs A: The GO enrichment of up-regulated DEGs; B: The GO enrichment of down-regulated DEGs.

Fig. 7 KEGG pathway enrichment of DEGs A: The KEGG pathway enrichment of up-regulated DEGs; B: The KEGG pathway enrichment of down- regulated DEGs.

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