Genomic insights into the serine protease gene family and expression profile analysis in the planthopper, Nilaparvata lugens

Bao, Yan-Yuan; Qin, Xia; Yu, Bing; Chen, Li-Bo; Wang, Zhe-Chao; Zhang, Chuan-Xi

doi:10.1186/1471-2164-15-507

Table 1 The genomic prediction of N. lugens serine protease and serine protease homologs

From: Genomic insights into the serine protease gene family and expression profile analysis in the planthopper, Nilaparvata lugens

Predicted gene	GenBank ID	Locus	Size (aa)	Exon	Orientation	HDS	Domains/Motifs	Best match	Similarity	E-value	Cover
Trypsin-like serine protease
Trypsin 1	KJ512112	scaffold574	334	7	+	active	Signal P	P. h.corporis	47%	1e-28	95%
Trypsin 2	KJ512113	scaffold261	360	7	-	active	Signal P	P. h.corporis	79%	5e-137	78%
Trypsin 3	KJ512114	scaffold998	299	6	-	active		P. h.corporis	62%	4e-91	99%
Trypsin 4	KJ512115	scaffold106	795	5	-	active	Signal P	P. h.corporis	84%	4e-178	41%
Trypsin 5	KJ512116	scaffold126	347	3	-	active	Signal P	P. h.corporis	69%	1e-114	90%
Trypsin 6	KJ512117	scaffold126	360	7	+	active	Signal P	P. h.corporis	79%	5e-137	78%
Trypsin 7	KJ512118	scaffold64	393	4	-	active	Signal P	P. h.corporis	89%	0	84%
Trypsin 8	KJ512119	scaffold260	323	5	+	active	Signal P	P. h.corporis	65%	3e-95	91%
Trypsin 9	KJ512120	scaffold189	318	12	-	active	Signal P	N.lugens	98%	0	100%
Trypsin 10	KJ512121	scaffold707	303	8	-	active	Signal P	N.lugens	54%	4e-58	79%
Trypsin 11	KJ512122	scaffold1712	290	5	+	active	Signal P	C.quinquefasciatus	54%	2e-46	92%
Trypsin 12	KJ512123	scaffold172	295	12	-	active	Signal P	A.mellifera	53%	6e-44	90%
Trypsin 13	KJ512124	scaffold6559	423	3	-	active	Signal P	D.pteronyssinus	59%	9e-50	77%
Trypsin 14	KJ512125	scaffold6559	287	1	-	active	Signal P	D.pteronyssinus	58%	1e-53	79%
Trypsin 15	KJ512126	scaffold6559	731	7	-	active	Signal P	D.pteronyssinus	61%	8e-66	99%
Trypsin 16	KJ512127	scaffold6559	262	2	-	active	Signal P	C.capitata	51%	2e-27	96%
Trypsin 17	KJ512128	scaffold50	318	6	+	active	Signal P	C.felis	59%	4e-64	89%
Trypsin 18	KJ512129	scaffold327	292	5	-	active	Signal P	A.mellifera	48%	5e-25	79%
Trypsin 19	KJ512130	scaffold126	511	7	-	active	Signal P	T.castaneum	68%	0	94%
Trypsin 20	KJ512131	scaffold577	294	1	+	active	Signal P	D.melanogaster	48%	5e-32	87%
Trypsin 21	KJ512132	scaffold1720	272	4	-	active		H. saltator	48%	4e-20	70%
Trypsin 22	KJ512133	scaffold1722	747	14	+	active		A.pisum	54%	2e-52	75%
Trypsin 23	KJ512134	scaffold299	260	6	-	inactive	Signal P	N.vitripennis	45%	4e-25	85%
Trypsin 24	KJ512135	scaffold299	290	5	-	inactive	Signal P	N.lugens	98%	0	94%
Trypsin 25	KJ512136	scaffold299	300	7	-	Inactive	Signal P	N.lugens	56%	4e-49	82%
Trypsin 26	KJ512137	scaffold299	292	5	-	Inactive	Signal P	N.lugens	50%	4e-53	84%
Trypsin 27	KJ512138	scaffold299	266	6	-	inactive	Signal P	N.vitripennis	45%	7e-25	97%
Trypsin 28	KJ512139	scaffold601	298	1	-	inactive	Signal P	T.castaneum	48%	3e-23	74%
Trypsin 29	KJ512140	scaffold682	325	6	+	inactive	Signal P	P. h.corporis	66%	3e-106	95%
Trypsin 30	KJ512141	scaffold2065	281	6	+	inactive	Signal P	D. yakuba	55%	6e-34	79%
Trypsin 31	KJ512142	scaffold4540	247	4	-	inactive		P. h.corporis	53%	2e-31	91%
Clotting serine proteases
Clotting factor C like	KJ512060	scaffold437	553	2	+	active	CCP	C.biroi	52%	1e-108	96%
Clotting factor B like	KJ512061	scaffold867	321	7	-	inactive	Signal P	B.impatiens	53%	1e-52	82%
Proclotting enzyme 1	KC355213	scaffold424	397	7	+	active	Clip	A.pisum	56%	4e-91	91%
Proclotting enzyme 2	KC355214	scaffold424	376	12	-	active	Clip	A.pisum	55%	6e-89	91%
Proclotting enzyme 3	KC355215	scaffold1854	460	9	-	active	Clip	C.floridanus	66%	4e-73	90%
Serine protease nudel
Serine protease nudel like	KJ512077	scaffold771	683	11	-	active	LDLA	A.pisum	47%	2e-86	97%
Serine protease gd
Serine protease gd like	KJ512078	scaffold50	441	10	+	active	Signal P	A.florea	57%	3e-96	94%
Serine protease snake
Serine protease snake 1	KC355219	scaffold407	363	7	+	active	Clip	A.pisum	54%	3e-74	89%
Serine protease snake 2	KC355220	scaffold183	406	5	-	active	Clip	A.pisum	50%	7e-71	99%
Serine protease snake 3	KC355221	scaffold183	406	7	-	active	Clip	A.pisum	47%	1e-71	99%
Serine protease snake 4	KC355222	scaffold3538	546	7	+	active	Clip	T.castaneum	58%	3e-65	95%
Serine protease snake 5	KC355223	scaffold407	358	8	-	inactive	Clip	A.pisum	41%	8e-31	89%
Serine protease snake 6	KC355224	scaffold407	374	7	-	inactive	Clip	A.pisum	45%	1e-33	93%
Serine protease snake 7	KC355225	scaffold407	362	7	-	active	Clip	A.pisum	53%	5e-70	85%
Serine protease snake 8	KJ512098	scaffold407	389	7	-	active		A.pisum	60%	1e-74	86%
Serine protease snake 9	KJ512099	scaffold407	489	6	+	active	Signal P	A.pisum	57%	4e-70	56%
Serine protease snake 10	KJ512100	scaffold407	367	7	-	active	Signal P	A.pisum	56%	3e-66	80%
Serine protease snake 11	KJ512101	scaffold4413	489	7	-	active	Signal P	A.pisum	60%	2e-69	56%
Serine protease snake 12	KJ512102	scaffold4413	389	6	+	active		A.pisum	55%	1e-74	86%
Serine protease easter
Serine protease easter 1	KJ512062	scaffold258	289	3	+	active		H. saltator	45%	3e-31	97%
Serine protease easter 2	KJ512063	scaffold258	319	6	+	active	Signal P	H. saltator	52%	2e-45	98%
Serine protease easter 3	KJ512064	scaffold258	397	7	+	active		N.vitripennis	51%	2e-27	61%
Serine protease easter 4	KJ512065	scaffold258	407	7	-	active	Signal P	H. saltator	49%	1e-41	76%
Serine protease easter 5	KJ512066	scaffold258	334	5	-	inactive	Signal P	H. saltator	45%	5e-19	80%
Serine protease easter 6	KJ512067	scaffold258	330	6	-	inactive	Signal P	H. saltator	45%	4e-30	92%
Serine protease easter 7	KJ512068	scaffold574	315	7	+	active	Signal P	H. saltator	52%	8e-50	92%
Serine protease easter 8	KJ512069	scaffold574	323	5	-	active	Signal P	H. saltator	48%	4e-35	98%
Serine protease easter 9	KJ512070	scaffold1012	318	6	+	inactive	Signal P	A.aegypti	43%	9e-17	80%
Serine protease easter 10	KJ512071	scaffold1012	356	6	+	inactive	Signal P	A.aegypti	43%	2e-17	90%
Serine protease easter 11	KJ512072	scaffold1012	322	7	+	active	Signal P	H. saltator	50%	5e-41	92%
Serine protease easter 12	KJ512073	scaffold1121	334	6	-	active	Signal P	H. saltator	62%	4e-72	85%
Serine protease easter 13	KJ512074	scaffold236	310	10	-	active	Signal P	H. saltator	52%	2e-43	94%
Serine protease easter 14	KJ512075	scaffold4778	307	8	-	active	Signal P	H. saltator	48%	2e-32	96%
Serine protease easter 15	KJ512076	scaffold4872	340	4	+	inactive	Signal P	A.mellifera	45%	5e-20	91%
Serine protease stubble
Serine protease stubble like 1	KJ512103	scaffold126	324	7	-	active	Signal P	M. rotundata	78%	9e-148	99%
Serine protease stubble like 2	KJ512104	scaffold126	371	7	+	active	Signal P	A.echinatior	55%	3e-32	70%
Serine protease stubble like 3	KJ512105	scaffold223	398	7	+	active	Signal P	B. mori	64%	8e-119	86%
Serine protease stubble like 4	KJ512106	scaffold115	368	7	-	active		H. saltator	79%	0	100%
Serine protease stubble like 5	KJ512107	scaffold886	467	5	+	inactive		M rotundata	62%	4e-129	84%
Serine protease
Serine protease 1	KJ512079	scaffold63	849	4	+	inactive		H. saltator	71%	2e-28	26%
Serine protease 2	KJ512080	scaffold1489	324	3	-	active	Signal P	B.mori	52%	4e-31	85%
Serine protease 3	KJ512081	scaffold219	743	11	+	active	MADF	A. pisum	93%	1e-141	64%
Serine protease 4	KJ512082	scaffold1220	550	4	+	active	CUB	A. pisum	57%	5e-137	88%
Serine protease 5	KJ512083	scaffold1208	492	10	+	active	CUB	A.pisum	74%	3e-93	83%
Serine protease 6	KJ512084	scaffold1877	258	4	+	inactive	Signal P	C.formosanus	47%	2e-20	75%
Serine protease 7	KJ512085	scaffold185	332	7	+	active	Signal P	D.mojavensis	55%	1e-49	74%
Serine protease 8	KJ512086	scaffold762	346	6	-	active		T.castaneum	65%	2e-83	88%
Serine protease HP21	KJ512089	scaffold2889	307	2	-	inactive	Signal P	T.castaneum	52%	1e-33	86%
Prophenoloxidase activating factor 1	KJ512096	scaffold66	390	7	-	inactive	Signal P	T.molitor	59%	2e-120	100%
Prophenoloxidase activating factor 2	KJ512097	scaffold66	395	6	-	inactive		T.molitor	69%	3e-123	83%
Hemolymph protease 1	KJ512090	scaffold972	314	1	-	inactive	Signal P	T.castaneum	47%	1e-32	86%
Hemolymph protease 2	KJ512091	scaffold236	314	6	-	inactive		C.quinquefasciatus	43%	7e-16	82%
Serine protease SP24D	KJ512092	scaffold2296	310	6	+	active	Signal P	C.quinquefasciatus	48%	1e-18	78%
Serine protease P69	KJ512093	scaffold598	708	8	+	active	Signal P	T.castaneum	69%	7e-84	61%
Serine protease HTRA2	KJ512094	scaffold552	420	7	+	active	PDZ	N.vitripennis	70%	5e-133	91%
Transmembrane serine protease
Serine protease 11	KJ512108	scaffold967	919	18	-	active	FRI & SR	T.castaneum	72%	0	86%
Ovochymase 1	KJ512109	scaffold305	322	7	+	active	TM	A.pisum	77%	3e-124	87%
Ovochymase 2	KJ512110	scaffold126	360	7	-	active	TM	T.castaneum	87%	3e-147	68%
Ovarian serine protease	KJ512111	scaffold498	1334	9	+	active	TM	T.castaneum	71%	2e-97	47%

Table 1 Identification of SP and SPH genes in the N. lugens genome. The SP and SPH sequences were obtained from the N. lugens transcriptome databases and genomic sequences, which were confirmed using the tBLASTX algorithm with a cut-off E-value of 10^-10. The genomic organization of exons and introns of the SP and SPH genes was predicted based on the mRNA-genome alignments at the NCBI spideyweb (http://www.ncbi.nlm.nih.gov/spidey/spideyweb.cgi). Locus, size and orientation indicate the location on scaffolds, predicted amino acids (aa) and the transcription orientation of the genes. HDS refers to the presence or absence of His, Asp and Ser residues in the catalytic triad, implying active or inactive proteases. A.pisum, Acyrthosiphon pisum; T. castaneum, Tribolium castaneum; P. h. corporis, Pediculus humanus corporis; B. mori, Bombyx mori; C.quinquefasciatus, Culex quinquefasciatus; C. capitata, Ceratitis capitata; H. saltator, Harpegnathos saltator; A. mellifera, Apis mellifera; M. rotundata, Megachile rotundata; A.echinatior, Acromyrmex echinatior; N. lugens, Nilaparvata lugens; C. felis, Ctenocephalides felis; D. pteronyssinus, Dermatophagoides pteronyssinus; D. melanogaster, Drosophila melanogaster; D.mojavensis, Drosophila mojavensis; D. yakuba, Drosophila yakuba; C. floridanus, Camponotus floridanus; A. florea, Apis florea; N.vitripennis, Nasonia vitripennis; A. aegypti, Aedes aegypti; B. impatiens, Bombus impatiens; T. molitor, Tenebrio molitor; C. formosanus, Coptotermes formosanus; C. biroi, Cerapachys biroi.

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ISSN: 1471-2164

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