Transcriptome and Candidate Effectors Analysis of Pratylenchus brachyurus

doi:10.13560/j.cnki.biotech.bull.1985.2022-0773

Abstract

Abstract:

Pratylenchus brachyurus is an important migratory endoparasitic phytopathogenic nematode. Analysis of the transcriptome is an important basis for further research on its parasitic characteristics and pathogenic mechanism. In the transcriptome of P. brachyurus, 72 516 unigenes were generated and 38 266（52.76%）unigenes were annotated against seven protein databases. In the carbohydrate-active enzymes analysis, 541 proteins were predicted to have plant/fungal cell wall degrading activities, and belonged to the families of GH5, GH30, GH53, GH28, PL3, GH16, GH18 and GH20 respectively. There were 56 protein sequences in the transcriptome demonstrating similarities with orthologues involved in RNAi pathway of Caenorhabditis elegans. Further analysis showed that 51 protein sequences with homology to known plant-parasitic nematode effector proteins were identified. Nine candidate effectors were selected and their potential ability in suppressing plant defense was tested. Seven of them suppressed programmed cell death（PCD）triggered by Gpa2/Rbp-1. The results revealed that the gene distribution characteristics of P. brachyurus were similar to of the same genus of Pratylenchus spp. The candidate effectors may play a critical role in suppressing plant defense.

Key words: Pratylenchus brachyurus, transcriptome, effector, programmed cell death

HU Li-li, LIN Bo-rong, WANG Hong-hong, CHEN Jian-song, LIAO Jin-ling, ZHUO Kan. Transcriptome and Candidate Effectors Analysis of Pratylenchus brachyurus[J]. Biotechnology Bulletin, 2023, 39(3): 254-266.

Figures/Tables 12

References 45

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Primer name	Primer sequence（5'-3'）	Application
45363F	ATGCTGTTCACCGCACTGCT	ORF amplification
45363R	TTATGTTCTCTTCACCTCGC	ORF amplification
39081F	ATGGTCTTCAAAAGCGCTTC	ORF amplification
39081R	CTAATGCTGTTTCATCATTC	ORF amplification
38325F	ATGCGTGCCAATTTGTTGTG	ORF amplification
38325R	TCAATTGAGGCAATCACGCT	ORF amplification
40687F	ATGCATCTAGTTCTATTACT	ORF amplification
40687R	TCAGTCACGTTTGGCCAACT	ORF amplification
41828F	ATGTTCCGCTGCTCTTCCTC	ORF amplification
41828R	TCATTCCTCCTCTCGGTTCT	ORF amplification
49596F	ATGGGCATTGGCTTGGCCAT	ORF amplification
49596R	TCAGACCAACGGGTACGACG	ORF amplification
50445F	ATGGCTACATCAATTTTTGT	ORF amplification
50445R	TCAAAAAGCGATGAATGCGA	ORF amplification
51705F	ATGCTTTCTTGCCGTCTCCTT	ORF amplification
51705R	TCAAATGGGATGATTCAACA	ORF amplification
41042F	ATGTTCTTTACTGTTGCTGG	ORF amplification
41042R	TCAAATTCGAAAGCGTTCAA	ORF amplification
828-1305F	TGACCATGGAAATTCCTGCTCGACAATTTGG	Vector construction
828-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCTTCCTCCTCTCGGTTCTCTC	Vector construction
363-1305F	TGACCATGGAACAACAGGAAAAATATCAGCC	Vector construction
363-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCTGTTCTCTTCACCTCGCCCT	Vector construction
081-1305F	TGACCATGGAA ATCGTCAGTGCGCTTCCCCG	Vector construction
081-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCATGCTGTTTCATCATTCCTG	Vector construction
325-1305F	TGACCATGGAA ATTGGCATTGGCCGAACGCA	Vector construction
325-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCATTGAGGCAATCACGCTCCT	Vector construction
687-1305F	TGACCATGGAA GCCAGCTGTGATTCGCCAAA	Vector construction
687-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCGTCACGTTTGGCCAACTGTT	Vector construction
596-1305F	TGACCATGGAA GTGCAATGGCGTGTTGAGCG	Vector construction
596-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCGACCAACGGGTACGACGCCT	Vector construction
445-1305F	TGACCATGGAA CAATCTCCCAATGCAGATAA	Vector construction
445-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAAAAGCGATGAATGCGACAG	Vector construction
705-1305F	TGACCATGGAA GAACAATACGATTCAACGGA	Vector construction
705-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAATGGGATGATTCAACAGGA	Vector construction
042-1305F	TGACCATGGAA CTGGGCTGTATGAGCACAAT	Vector construction
042-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAATTCGAAAGCGTTCAATCA	Vector construction

Primer name	Primer sequence（5'-3'）	Application
45363F	ATGCTGTTCACCGCACTGCT	ORF amplification
45363R	TTATGTTCTCTTCACCTCGC	ORF amplification
39081F	ATGGTCTTCAAAAGCGCTTC	ORF amplification
39081R	CTAATGCTGTTTCATCATTC	ORF amplification
38325F	ATGCGTGCCAATTTGTTGTG	ORF amplification
38325R	TCAATTGAGGCAATCACGCT	ORF amplification
40687F	ATGCATCTAGTTCTATTACT	ORF amplification
40687R	TCAGTCACGTTTGGCCAACT	ORF amplification
41828F	ATGTTCCGCTGCTCTTCCTC	ORF amplification
41828R	TCATTCCTCCTCTCGGTTCT	ORF amplification
49596F	ATGGGCATTGGCTTGGCCAT	ORF amplification
49596R	TCAGACCAACGGGTACGACG	ORF amplification
50445F	ATGGCTACATCAATTTTTGT	ORF amplification
50445R	TCAAAAAGCGATGAATGCGA	ORF amplification
51705F	ATGCTTTCTTGCCGTCTCCTT	ORF amplification
51705R	TCAAATGGGATGATTCAACA	ORF amplification
41042F	ATGTTCTTTACTGTTGCTGG	ORF amplification
41042R	TCAAATTCGAAAGCGTTCAA	ORF amplification
828-1305F	TGACCATGGAAATTCCTGCTCGACAATTTGG	Vector construction
828-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCTTCCTCCTCTCGGTTCTCTC	Vector construction
363-1305F	TGACCATGGAACAACAGGAAAAATATCAGCC	Vector construction
363-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCTGTTCTCTTCACCTCGCCCT	Vector construction
081-1305F	TGACCATGGAA ATCGTCAGTGCGCTTCCCCG	Vector construction
081-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCATGCTGTTTCATCATTCCTG	Vector construction
325-1305F	TGACCATGGAA ATTGGCATTGGCCGAACGCA	Vector construction
325-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCATTGAGGCAATCACGCTCCT	Vector construction
687-1305F	TGACCATGGAA GCCAGCTGTGATTCGCCAAA	Vector construction
687-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCGTCACGTTTGGCCAACTGTT	Vector construction
596-1305F	TGACCATGGAA GTGCAATGGCGTGTTGAGCG	Vector construction
596-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCGACCAACGGGTACGACGCCT	Vector construction
445-1305F	TGACCATGGAA CAATCTCCCAATGCAGATAA	Vector construction
445-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAAAAGCGATGAATGCGACAG	Vector construction
705-1305F	TGACCATGGAA GAACAATACGATTCAACGGA	Vector construction
705-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAATGGGATGATTCAACAGGA	Vector construction
042-1305F	TGACCATGGAA CTGGGCTGTATGAGCACAAT	Vector construction
042-1305R	TCACACGTGTTACTTATCGTCGTCATCCTTGTAATCAATTCGAAAGCGTTCAATCA	Vector construction

Data	Total reads/bp	Total base pairs/bp	Average length/bp	Length range/bp	N50/bp	N90/bp
Raw reads	33 691 610	4 211 451 250	-	-	-	-
Clean reads>200 bp	33 268 909	4 158 613 625	-	-	-	-
Transcripts	101 595	80 122 468	789	200-15 754	1 284	1 131
Unigenes	72 516	50 829 031	701	200-15 754	311	276

Data	Total reads/bp	Total base pairs/bp	Average length/bp	Length range/bp	N50/bp	N90/bp
Raw reads	33 691 610	4 211 451 250	-	-	-	-
Clean reads>200 bp	33 268 909	4 158 613 625	-	-	-	-
Transcripts	101 595	80 122 468	789	200-15 754	1 284	1 131
Unigenes	72 516	50 829 031	701	200-15 754	311	276

Sequence file	NR	NT	Swiss-Prot	KEGG	PFAM	GO	KOG	ALL
Number	31 374	3 314	24 164	13 521	29 265	29 729	19 183	72 516
Percentage/%	43.26	4.57	33.32	18.64	40.35	40.99	26.45	100