Transcriptome Analysis of Amorphophallus konjac with Different Root Barriers

doi:10.7668/hbnxb.20193441

Abstract

Abstract:

The study aims to understand the biological process and metabolic pathway of konjac under different root separation modes from black locust,in order to provide molecular basis for the expression regulation and response mechanism of related genes in intercropping konjac roots.Illumina NovaSeq 6000 sequencing technology was used for transcriptome analysis of konjac roots separated by plastic membrane(FS),nylon mesh(MS),and non-separation(NS).A total of 59.82 Gb data were obtained,and 92 358 transcript sequences corresponding to 40 122 Unigenes were generated after de novo assembly and quantitative assessment.The most annotated Unigene in the NCBI-Nr database was 23 960,accounting for 59.72% of the total Unigenes.The transcriptome data were pair-wise compared,and the total quantities of differential expression genes of FS_vs_MS,FS_vs_NS and MS_vs_NS were 1 776,733 and 896,respectively.Of which,their corresponding up-regulated genes accounted for 33.1%,22.8% and 50.8%.GO enrichment analysis indicated that significantly differential expressed genes were mainly involved in plasma membrane,cell membrane,cell periphery,cell wall,encapsulating structure,intrinsic components of membrane,and intrinsic components of plasma membrane.KEGG enrichment analysis showed that the ribosome,oxidative phosphorylation and plant hormone signal transduction were the most significant metabolic pathways in the roots of konjac separated by nylon mesh and non-separation compared with plastic membrane.Transcriptome analysis of konjac roots provided the basic data for studying response mechanism of intercropping konjac.

Key words: Konjac, Intercropping, Transcriptome, DEGs

HE Fei, LI Chuan, SHAH Faisal, LIU Fuqiang, DUAN Yuanpeng, WANG Meng, RUAN Jia, WEI Menglin, JIANG Hao, MA Xingguang, WANG Zhuo. Transcriptome Analysis of Amorphophallus konjac with Different Root Barriers[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(2): 65-74. doi: 10.7668/hbnxb.20193441.

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References 32

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序号 No.	基因ID Gene ID	正向引物序列(5'-3') Forward primer sequence(5'-3')	反向引物序列(5'-3') Reverse primer sequence(5'-3')
1	TRINITY_DN5161_c0_g1	CTCTTCGTCTCGCTGGCAA	GGATGATCGGCATCGACCC
2	TRINITY_DN1055_c0_g1	AGTCGGACAACTGCTCCTTG	CCGAACACTTGTTGCCCTTG
3	TRINITY_DN41977_c0_g2	TGATGTGCACTAGCACCGAG	TAAGCCTGCTGGCATCATGT
4	TRINITY_DN1454_c0_g1	CCAGGCAGAAGAAGACCGTT	GCAGCGTACCACCAGTACAT
5	TRINITY_DN22369_c0_g1	CGGTGTCCGAAGACCATCAT	ATTTGGTTGAGGAGCTGGCA
6	TRINITY_DN1700_c0_g1	GTCCGCTTCTAGCACTCCTC	CACGAGATAGGCATCCGACC
7	EF1-a	AAGTTCCTGAAGAATGGCGAT	GTCCCTCACGGCAAACCTACC

序号 No.	基因ID Gene ID	正向引物序列(5'-3') Forward primer sequence(5'-3')	反向引物序列(5'-3') Reverse primer sequence(5'-3')
1	TRINITY_DN5161_c0_g1	CTCTTCGTCTCGCTGGCAA	GGATGATCGGCATCGACCC
2	TRINITY_DN1055_c0_g1	AGTCGGACAACTGCTCCTTG	CCGAACACTTGTTGCCCTTG
3	TRINITY_DN41977_c0_g2	TGATGTGCACTAGCACCGAG	TAAGCCTGCTGGCATCATGT
4	TRINITY_DN1454_c0_g1	CCAGGCAGAAGAAGACCGTT	GCAGCGTACCACCAGTACAT
5	TRINITY_DN22369_c0_g1	CGGTGTCCGAAGACCATCAT	ATTTGGTTGAGGAGCTGGCA
6	TRINITY_DN1700_c0_g1	GTCCGCTTCTAGCACTCCTC	CACGAGATAGGCATCCGACC
7	EF1-a	AAGTTCCTGAAGAATGGCGAT	GTCCCTCACGGCAAACCTACC

样品 Sample	原始序列数 Raw reads	原始碱基数 Raw bases	高质量序列 (占原始序列数比例/%) Clean reads (ratio)	高质量碱基 Clean bases	Q20/%	Q30/%
NS_1	46 227 980	6 934 197 000	40 747 808 (88.14)	6 112 171 200	96.55	92.35
NS_2	51 960 372	7 794 055 800	47 854 830 (92.09)	7 178 224 500	96.80	92.67
NS_3	56 569 902	8 485 485 300	52 236 882 (92.34)	7 835 532 300	96.54	92.08
MS_1	45 908 894	6 886 334 100	41 795 366 (91.03)	6 269 304 900	96.82	92.66
MS_2	46 103 366	6 915 504 900	41 337 718 (89.66)	6 200 657 700	96.79	92.64
MS_3	52 066 606	7 809 990 900	45 207 718 (86.82)	6 781 157 700	96.44	92.08
FS_1	50 236 112	7 535 416 800	44 801 948 (89.18)	6 720 292 200	96.50	92.04
FS_2	44 203 706	6 630 555 900	40 561 598 (91.76)	6 084 239 700	96.89	92.81
FS_3	49 690 406	7 453 560 900	44 279 090 (89.10)	6 641 863 500	96.49	92.22

样品 Sample	原始序列数 Raw reads	原始碱基数 Raw bases	高质量序列 (占原始序列数比例/%) Clean reads (ratio)	高质量碱基 Clean bases	Q20/%	Q30/%
NS_1	46 227 980	6 934 197 000	40 747 808 (88.14)	6 112 171 200	96.55	92.35
NS_2	51 960 372	7 794 055 800	47 854 830 (92.09)	7 178 224 500	96.80	92.67
NS_3	56 569 902	8 485 485 300	52 236 882 (92.34)	7 835 532 300	96.54	92.08
MS_1	45 908 894	6 886 334 100	41 795 366 (91.03)	6 269 304 900	96.82	92.66
MS_2	46 103 366	6 915 504 900	41 337 718 (89.66)	6 200 657 700	96.79	92.64
MS_3	52 066 606	7 809 990 900	45 207 718 (86.82)	6 781 157 700	96.44	92.08
FS_1	50 236 112	7 535 416 800	44 801 948 (89.18)	6 720 292 200	96.50	92.04
FS_2	44 203 706	6 630 555 900	40 561 598 (91.76)	6 084 239 700	96.89	92.81
FS_3	49 690 406	7 453 560 900	44 279 090 (89.10)	6 641 863 500	96.49	92.22

长度范围 Length range	转录本 Transcript	单一基因 Unigene
总数量Total number	92 358.00	40 122.00
总长度/bp Total length	96 731 890.00	36 605 858.00
N50长度/bp N50 length	1 478.00	1 441.00
平均长度/bp Mean length	1 047.36	912.36
GC/%	48.49	49.36

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