Mining sequences with similarity to XTH genes in the Solanum tuberosum L. transcriptome: introductory step for identifying homologous XTH genes

Figures & data

Table 1. Putatively homologous XTH genes from the Solanum tuberosum RNAseq database.

Sequence name	E-value	Similarity mean (%)	Bit-Score	Putative homologous XTH gene in Arabidopsis thaliana^Citation1	Putative homologous XTH in Solanum lycopersicum ^1
PGSC0003DMG400041434	1.11189E-22	63.66	156.4	-	SlXTH19
PGSC0003DMG400042833	3.41499E-36	65.63	212.2	AtXTH1/AtXTH2	SlXTH7
PGSC0003DMG400001229	1.44952E-42	60.59	286.6	AtXTH3	SlXTH4
PGSC0003DMG400002188	7.09171E-69	65.91	299.7	AtXTH4-1	SlXTH4
PGSC0003DMG400024755	8.73328E-70	66.63	294.3	AtXTH5-1	SlXTH1
PGSC0003DMG402010181	4.33809E-63	54.05	229.9	AtXTH5-2	SlXTH18
PGSC0003DMG402010918	5.90652E-64	66.53	243.0	AtXTH5-3	SlXTH4
PGSC0003DMG400021398	1.12747E-75	67.99	239.2	AtXTH7	SlXTH7
PGSC0003DMG400002084	2.91162E-59	54.69	211.1	AtXTH8	SlXTH23
PGSC0003DMG400024060	8.36804E-71	61.67	306.6	AtXTH8	SlXTH15-2
PGSC0003DMG400011281	9.85939E-16	91.43	124.0	AtXTH8	SlXTH15-1
PGSC0003DMG400026189	1.00497E-89	61.97	318.2	AtXTH9-2	SlXTH16
PGSC0003DMG400005127	4.29487E-60	59.03	144.8	AtXTH10-1	SlXTH7
PGSC0003DMG400017299	5.34064E-93	63.77	171.0	AtXTH15	SlXTH10
PGSC0003DMG400031101	6.93065E-94	65.19	171.8	AtXTH15	SlXTH10
PGSC0003DMG400021877	5.64726E-57	69.87	260.4	AtXTH15	SlXTH12
PGSC0003DMG400017298	1.58365E-53	69.82	291.6	AtXTH16	SlXTH9
PGSC0003DMG400004670	7.39946E-56	25812	260.8	AtXTH16	SlXTH3
PGSC0003DMG401018740	1.26591E-40	63.48	237.7	AtXTH22	SlXTH13
PGSC0003DMG402018740	1.08367E-55	70.22	284.6	AtXTH22	SlXTH3
PGSC0003DMG400024121	4.36905E-23	72.95	134.0	AtXTH22	SlXTH10
PGSC0003DMG400002309	2.24189E-89	62.1	161.4	AtXTH22	SlXTH11
PGSC0003DMG400014823	9.64778E-106	67.05	250.8	AtXTH23	SlXTH3
PGSC0003DMG400013975	2.05102E-53	68.65	251.9	AtXTH23	SlXTH2
PGSC0003DMG400007794	2.54537E-61	61.28	235.3	AtXTH24	SlXTH9
PGSC0003DMG400007854	9.06518E-61	61.11	236.1	AtXTH24	SlXTH9
PGSC0003DMG400018741	4.50311E-57	83.13	229.6	AtXTH25	SlXTH20
PGSC0003DMG400029503	2.13033E-67	59.27	319.3	AtXTH28	SlXTH8
PGSC0003DMG400022791	1.19207E-67	57.83	333.6	AtXTH28	SlXTH8
PGSC0003DMG400001809	5.07525E-63	58.3	337.8	AtXTH30	SlXTH5
PGSC0003DMG400009300	3.39019E-56	59.08	389.8	AtXTH30	SlXTH5
PGSC0003DMG400014024	1.64996E-40	68.94	161.4	AtXTH31	SlXTH6
PGSC0003DMG400000408	5.57005E-46	70.39	216.9	AtXTH31	SlXTH6
PGSC0003DMG400003432	1.61541E-33	65.02	256.4	-	SlXTH6
PGSC0003DMG400036031	3.00177E-14	62.97	236.3	-	SlXTH6
PGSC0003DMG400003434	5.11064E-48	50.48	117.9	AtXTH32-1	SlXTH6
PGSC0003DMG400003866	2.11514E-65	65.16	271.9	AtXTH32-2	SlXTH14
PGSC0003DMG400004109	3.54934E-52	52.48	297.0	AtXTH33	SlXTH25
PGSC0003DMG400004599	1.57405E-11	60.87	265.6	-	SlXTH23
PGSC0003DMG400029203	2.54838E-12	72.34	326.8	-	SlXTH23

¹based on NCBI and EggNOG (St = Solanum tuberosum); different numbers after several gene names indicate orthologs or putatively homologous sequences for the same gene which were identified from S. tuberosum RNAseq data.

Table 2. The response of the putatively homologous StXTH genes to different ultrasound treatments.

Sequence name	Putative XTH gene in Solanum lycopersicum ^1	Response to different ultrasound treatments^Citation2
		Up-regulation	Down-regulation
PGSC0003DMG400024755	StXTH1		(2.74) AB-24 h vs. PE-24 h
			(2.26) CPE-4 w vs. PE-4 w
PGSC0003DMG400013975	StXTH2		(4.06) CPE-1 w vs. PE-1 w
PGSC0003DMG400014823	StXTH3-1 StXTH3-2 StXTH3-3 StXTH3-4		(3.32) CPE-4 w vs. PE-4 w
			(1.87) CAB-4 w vs. AB-4 w
PGSC0003DMG400001809	StXTH5		(1.26) AB-1 w vs. PE-1 w
PGSC0003DMG400014024	StXTH6-1		(6.77) AB-24 h vs. PE-24 h
PGSC0003DMG400000408	StXTH6-2	(−1.43) CPE-4 w vs. PE-4 w	(3.01) AB-24 h vs. PE-24 h
			(1.51) AB-1 w vs. PE-1 w
			(2.03) CPE-24 h vs. PE-24 h
			(3.27) CPE-1 w vs. PE-1 w
PGSC0003DMG400021398	StXTH7		(2.66) AB-48 h vs. PE-48 h
			(1.66) CPE-48 h vs. PE-48 h
PGSC0003DMG400017298	StXTH9-1	(−2.45) CAB-24 h vs. AB-24 h	(3.86) AB-24 h vs. PE-24 h
			(3.53) AB-1 w vs. PE-1 w
			(3.86) CPE-1 w vs. PE-1 w
			(4.20) CAB-48 h vs. AB-48 h
PGSC0003DMG400007854	StXTH9-2		(2.57) AB-24 h vs. PE-24 h
PGSC0003DMG400017299	StXTH10		(2.54) CPE-4 w vs. PE-4 w
PGSC0003DMG400021877	StXTH12	(−2.69) CAB-0 h vs. AB-0 h
PGSC0003DMG400026189	StXTH16	(−2.50) CAB-0 h vs. AB-0 h
PGSC0003DMG400004109	StXTH25	(−1.82) CAB-24 h vs. AB-24 h

¹based on NCBI and EggNOG (St = Solanum tuberosum); different numbers after several gene names indicate orthologs or putatively homologous sequences for the same gene which were identified from S. tuberosum RNAseq data (Table 1). Names of the StXTH genes are based on the corresponding SlXTHs.

²AB, air-based US;^5,23 C, control (no US treatment); h, hours; PE, liquid-based US;⁷ US, ultrasound; w, weeks; number in brackets indicate the change in expression intensity in the different US treatment comparisons.

h, hour; w, week

Figure 1. Phylogenetic tree of XTH genes from Arabidopsis thaliana (L.) Heynh. (AtXTH), Solanum lycopersicum L. (SlXTH) and putative XTH genes from Solanum tuberosum L. (StXTH). The phylogenetic tree was constructed by the neighbor-joining method with 5000 bootstrap replications using MEGA X.

Gagliano M, Mancuso S, Robert D. Towards understanding plant bioacoustics. Trends Plant Sci. 2012;17:1–7. doi:10.1016/j.tplants.2012.03.002.

 PubMed Web of Science ®Google Scholar

Gagliano M. Green symphonies: a call for studies on acoustic communication in plants. Behav Ecol. 2013;24:789–796. doi:10.1093/beheco/ars206.

 PubMed Web of Science ®Google Scholar

Dobránszki J, Hidvégi N, Gulyás A, Teixeira da Silva JA. mRNA transcription profile of potato (Solanum tuberosum L.) exposed to ultrasound during different stages of in vitro plantlet development. Plant Mol Biol. 2019;100:511–525. doi:10.1007/s11103-019-00876-0.

 PubMed Web of Science ®Google Scholar

Dobránszki J, Hidvégi N, Gulyás A, Tóth B, Teixeira da Silva JA. Transcription profile of potato (Solanum tuberosum L.) growing in vitro. J Plant Growth Regul. 2020a. doi:10.1007/s00344-020-10133-0.

 Web of Science ®Google Scholar

Teixeira da Silva JA, Hidvégi N, Gulyás A, Tóth B, Dobránszki J. Transcriptomic response of in vitro potato (Solanum tuberosum L.) to piezoelectric ultrasound. Plant Mol Biol Rep. 2020. doi:10.1007/s11105-020-01204-3.

 PubMed Web of Science ®Google Scholar