The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection
Abstract
:1. Introduction
2. Results and Discussion
2.1. Complete Genome Sequencing, Assembly and Annotation
Strain | Chr1_ID | Length | Gen# | Chr2_ID | Length | Gen# | CG% |
---|---|---|---|---|---|---|---|
* B. abortus A13334 | NC_016795.1 | 2,123,773 | 2086 | NC_016777.1 | 1,162,259 | 1102 | 57.40 |
B. abortus bv.1 str 9-941 | NC_006932.1 | 2,124,241 | 2082 | NC_006933.1 | 1,162,204 | 1103 | 57.22 |
B. abortus S19 | NC_010742.1 | 2,122,487 | 2089 | NC_010740.1 | 1,161,449 | 1106 | 57.22 |
B. canis ATCC 23365 | NC_010103.1 | 2,105,969 | 2022 | NC_010104.1 | 1,206,800 | 1131 | 57.24 |
B. canis HSKA 52141 | NC_016778.1 | 2,107,023 | 2019 | NC_016796.1 | 1,170,489 | 1098 | 57.24 |
B. melitensis 16M | NC_003317.1 | 2,117,144 | 2040 | NC_003318.1 | 1,177,787 | 1107 | 57.22 |
B. melitensis ATCC 23457 | NC_012441.1 | 2,125,701 | 2059 | NC_012442.1 | 1,185,518 | 1117 | 57.22 |
B. melitensis biovar Abortus 2308 | NC_007618.1 | 2,121,359 | 2086 | NC_007624.1 | 1,156,948 | 1104 | 57.22 |
B. melitensis M28 | NC_017244.1 | 2,126,133 | 2058 | NC_017245.1 | 1,185,615 | 1118 | 57.22 |
B. melitensis M5-90 | NC_017246.1 | 2,126,451 | 2062 | NC_017247.1 | 1,185,778 | 1118 | 57.22 |
B. melitensis NI | NC_017248.1 | 2,117,717 | 2051 | NC_017283.1 | 1,176,758 | 1112 | 57.23 |
B. microti CCM 4915 | NC_013119.1 | 2,117,050 | 2024 | NC_013118.1 | 1,220,319 | 1135 | 57.25 |
B. ovis ATCC 25840 | NC_009505.1 | 2,111,370 | 2068 | NC_009504.1 | 1,164,220 | 1122 | 57.19 |
B. pinnipedialis B2/94 | NC_015857.1 | 2,138,342 | 2081 | NC_015858.1 | 1,260,926 | 1188 | 57.20 |
B. suis 1330 | NC_017251.1 | 2,107,783 | 2014 | NC_017250.1 | 1,207,380 | 1130 | 57.25 |
* B. suis ATCC 23445 | NC_010169.1 | 1,923,763 | 1848 | NC_010167.1 | 1,400,844 | 1327 | 57.21 |
B. suis VBI22 | NC_016797.1 | 2,108,637 | 2015 | NC_016775.1 | 1,207,451 | 1132 | 57.25 |
B. suis 019 | CP013963.1 | 2,098,391 | 1972 | CP013964.1 | 1,204,433 | 1119 | 57.27 |
2.2. Phylogenetic Analysis
2.3. Comparative Genome Analysis Using 16 Complete Genomes
Gene-ID | Chr | Length | Copy | Product |
---|---|---|---|---|
BSS2_I0512 | 1 | 795 | 1 | integrase catalytic subunit |
BSS2_I0517 | 1 | 1119 | >1 | mannosyltransferase |
BSS2_I0518 | 1 | 369 | 1 | transposase |
BSS2_I0519 | 1 | 342 | 1 | IS5 family transposase orfB |
BSS2_I0898 | 1 | 165 | >1 | hypothetical protein |
BSS2_I1794 | 1 | 1929 | 1 | hypothetical protein |
BSS2_I1795 | 1 | 675 | 1 | hypothetical protein |
BSS2_II0527 | 2 | 1965 | >1 | cell wall surface protein |
chr1_239 | 1 | 2232 | 1 | gtp pyrophosphokinase rsh |
chr1_277 | 1 | 1140 | 1 | cytochrome c-type biogenesis protein |
chr1_995 | 1 | 4782 | 1 | outer membrane autotransporter barrel domain-containing protein |
chr1_1847 | 1 | 777 | 1 | 3-mercaptopyruvate sulfurtransferase |
2.4. Beta-Ketoadipate Pathway and Lipopolysaccharide
1330-ID | Chr | Start | End | 019-ID | Start | End | Product |
---|---|---|---|---|---|---|---|
BRA0636 | 2 | 617674 | 618876 | chr2_454 | 490638 | 491840 | beta-ketoadipyl CoA thiolase |
BRA0637 | 2 | 618885 | 619574 | chr2_453 | 489940 | 490629 | 3-oxoadipate CoA-transferase, beta subunit |
BRA0638 | 2 | 619571 | 620278 | chr2_452 | 489236 | 489943 | 3-oxoadipate CoA-transferase, alpha subunit |
BRA0639 | 2 | 620462 | 621232 | chr2_451 | 488282 | 489052 | transcriptional regulator PcaR, putative |
BRA0640 | 2 | 621239 | 622156 | chr2_450 | 487358 | 488275 | pobR protein |
BRA0641 | 2 | 622269 | 623438 | chr2_449 | 486076 | 487245 | p-hydroxybenzoate hydroxylase |
BRA0642 | 2 | 623848 | 624756 | chr2_448 | 484758 | 485666 | transcriptional regulator PcaQ |
BRA0643 | 2 | 624850 | 625653 | chr2_447 | 483861 | 484664 | 3-oxoadipate enol-lactone hydrolase |
BRA0644 | 2 | 625657 | 626073 | chr2_446 | 483441 | 483860 | 4-carboxymuconolactone decarboxylase |
BRA0645 | 2 | 626070 | 626810 | chr2_445 | 482704 | 483444 | protocatechuate 3,4-dioxygenase, beta subunit |
BRA0646 | 2 | 626812 | 627429 | chr2_444 | 482085 | 482702 | protocatechuate 3,4-dioxygenase, alpha subunit |
BRA0647 | 2 | 627433 | 628497 | chr2_443 | 481017 | 482081 | 3-carboxy-cis,cis-muconate cycloisomerase, putative |
BRA1155 | 2 | 1155255 | 1156661 | chr2_1084 | 1157262 | 1158668 | aldehyde dehydrogenase family protein |
BRA1156 | 2 | 1156818 | 1157627 | chr2_1082 | 1156296 | 1157105 | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase |
BRA1157 | 2 | 1157694 | 1157804 | chr2_1081x | 1156119 | 1156229 | hypothetical protein |
BRA1158 | 2 | 1157845 | 1158648 | chr2_1081 | 1155275 | 1156078 | 2-keto-4-pentenoate hydratase |
BRA1159 | 2 | 1158652 | 1159518 | chr2_1080 | 1154405 | 1155271 | fumarylacetoacetate hydrolase family protein |
BRA1160 | 2 | 1159587 | 1160567 | chr2_1078 | 1153356 | 1154336 | catechol 2,3-dioxygenase (pseudo) |
BRA1161 | 2 | 1160622 | 1162136 | chr2_1077 | 1151787 | 1153301 | 5-carboxy-2-hydroxymuconate semialdehyde dehydrogenase |
BRA1162 | 2 | 1162206 | 1162598 | chr2_1076 | 1151325 | 1151717 | 5-carboxymethyl-2-hydroxymuconate delta isomerase |
BR0058 | 1 | 64824 | 66455 | chr1_179 | 820216 | 821847 | phosphoglucomutase |
BR0510 | 1 | 509856 | 511724 | chr1_359 | 374961 | 376829 | epimerase/dehydratase, putative |
BR0511 | 1 | 511711 | 512718 | chr1_358 | 373967 | 374974 | glycosyl transferase, group 4 family protein |
BR0517 * | 1 | 516587 | 517366 | chr1_353 | 369319 | 370098 | formyltransferase, putative |
BR0519 * | 1 | 518244 | 519002 | chr1_351 | 367683 | 368441 | O-antigen export system ATP-binding protein RfbE |
BR0520 | 1 | 518999 | 519781 | chr1_350 | 366904 | 367686 | O-antigen export system permease protein RfbD |
BR0521 | 1 | 519796 | 520899 | chr1_349 | 365786 | 366889 | perosamine synthase, putative |
BR0522 | 1 | 520907 | 521995 | chr1_348 | 364690 | 365778 | GDP-mannose 4,6-dehydratase |
BR0529 | 1 | 525257 | 526375 | NA | 498887 | 498927 | mannosyltransferase, putative |
BR0537 | 1 | 529702 | 531039 | chr1_345 | 361179 | 362516 | phosphomannomutase, putative |
BR0538 * | 1 | 531064 | 532488 | chr1_344 | 359730 | 361154 | mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase |
BR0539 * | 1 | 532521 | 533693 | chr1_343 | 358525 | 359697 | mannose-6-phosphate isomerase |
BR0540 | 1 | 533776 | 534885 | chr1_342 | 357333 | 358442 | glycosyl transferase, group 1 family protein |
BR0615 | 1 | 606884 | 608995 | chr1_269 | 283223 | 285334 | membrane protein, putative |
BR0981 | 1 | 948161 | 949393 | chr1_1915 | 2041237 | 2042469 | glycosyl transferase WboA |
BR0982 | 1 | 949390 | 950949 | chr1_1914 | 2039681 | 2041240 | glycosyl transferase, group 1 family protein |
BR1503 * | 1 | 1457802 | 1458866 | chr1_1441 | 1531664 | 1532728 | lipopolysaccharide core biosynthesis mannosyltransferase LpcC |
BRA0347 * | 2 | 326808 | 328223 | chr2_723 | 778336 | 779751 | mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase |
BRA0348 | 2 | 328220 | 329653 | chr2_722 | 776906 | 778339 | phosphoglucomutase, putative |
3. Materials and Methods
3.1. Sample Preparation, DNA-seq Library Construction
3.2. Draft Genome Sequencing, Assembly and Annotation
3.3. Complete Genome Sequencing, Assembly and Annotation
3.4. Phylogenetic Analysis Using Homologous Genes
3.5. Comparative Genome Analysis Using 16 Complete Genomes
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
NGS | Next-generation sequencing |
LCBs | Locally Collinear Blocks |
LPS | Lipopolysaccharide |
O-PS | O-polysaccharide |
GO | Gene Ontology |
UPGMA | unweighted pair-group method with arithmetic means |
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Wang, Y.; Wang, Z.; Chen, X.; Zhang, H.; Guo, F.; Zhang, K.; Feng, H.; Gu, W.; Wu, C.; Ma, L.; et al. The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection. Genes 2016, 7, 7. https://doi.org/10.3390/genes7020007
Wang Y, Wang Z, Chen X, Zhang H, Guo F, Zhang K, Feng H, Gu W, Wu C, Ma L, et al. The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection. Genes. 2016; 7(2):7. https://doi.org/10.3390/genes7020007
Chicago/Turabian StyleWang, Yuanzhi, Zhen Wang, Xin Chen, Hui Zhang, Fei Guo, Ke Zhang, Hanping Feng, Wenyi Gu, Changxin Wu, Lei Ma, and et al. 2016. "The Complete Genome of Brucella Suis 019 Provides Insights on Cross-Species Infection" Genes 7, no. 2: 7. https://doi.org/10.3390/genes7020007