198:
horizontally transferred. The alternative explanations are (i) that the region was present in the common ancestor but has been lost in all the other species being compared, or (ii) that the region was absent in the common ancestor but was acquired through mutation and selection in the species in which it is still found. The argument for multiple deletions of the region would be strengthened if there is evidence from outgroups that the region was present in the common ancestor, or if the phylogeny implies relatively few actual deletion events would be required. The argument for acquisition via mutation would be strengthened if the species with the region is known to have diverged substantially from the other species, or if the region in question is small. The plausibility of either (i) or (ii) would be modified if taxon sampling omitted many extinct species that may have possessed the region, and particularly if extinction was correlated with the presence of the region.
25:
191:
transferred. Two major problems with these methods are that false predictions can occur due to natural variation in the genome (sometimes due to highly expressed genes) and that horizontally transferred DNA will ameliorate (change to the host genome) over time; therefore, limiting predictions to only recently acquired GIs.
197:
based methods try to identify regions that show signs that they have been horizontally transferred using information from several related species. For example, a genomic region that is present in one species, but is not present in several other related species suggests that the region may have been
190:
Sequence based methods depend on the naturally occurring variation that exists between the genome sequence composition of different species. Genomic regions that show abnormal sequence composition (such as nucleotide bias or codon bias) suggests that these regions may have been horizontally
253:(ICEs), can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients. While excision is dependent on the ICE machinery present, integration is attributed to integrases present on the genomic islands.
1012:
153:, and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. For example, a GI associated with pathogenesis is often called a
169:
estimations.Genomic island is an segment of genome that are thought to have originated from horizontal transfer method. Genomic Island was first discovered by Hacker etal in 2000
1005:
998:
511:
250:
697:
684:
178:
161:
are referred to as antibiotic resistance islands. The same GI can occur in distantly related species as a result of various types of
707:
183:
Various genomic island predictions programs have been developed. These tools can be broadly grouped into sequence based methods and
108:
1835:
504:
42:
1666:
1261:
313:
Juhas, Mario; van der Meer, Jan Roelof; Gaillard, Muriel; Harding, Rosalind M; Hood, Derek W; Crook, Derrick W (March 2009).
89:
46:
61:
1802:
738:
584:
571:
1450:
1370:
1126:
214:
68:
855:
497:
35:
1671:
743:
75:
1518:
1419:
1336:
483:
270:
Langille, MG; Hsiao, WW; Brinkman, FS (May 2010). "Detecting genomic islands using bioinformatics approaches".
218:
162:
158:
372:"IslandViewer: an integrated interface for computational identification and visualization of genomic islands"
165:(transformation, conjugation, transduction). This can be determined by base composition analysis, as well as
1545:
1321:
549:
524:
489:
238:
234:
201:
One example of a method that integrates several of the most accurate GI prediction methods is IslandViewer.
57:
1773:
1089:
979:
907:
800:
1830:
1533:
1506:
825:
775:
835:
957:
875:
1477:
1472:
1348:
952:
865:
780:
666:
528:
194:
184:
154:
1713:
1555:
1511:
1467:
1205:
730:
601:
1763:
902:
810:
785:
629:
295:
226:
1758:
1462:
880:
458:
440:
401:
352:
334:
287:
134:
845:
795:
790:
221:
are located on genomic islands. These "islands" are characterised by their large size(>10
1494:
1388:
1021:
964:
894:
820:
770:
532:
448:
432:
391:
383:
342:
326:
279:
82:
815:
720:
479:
1751:
1445:
1424:
1353:
1156:
840:
675:
647:
616:
611:
436:
1741:
1628:
1499:
1358:
1146:
1076:
805:
762:
590:
580:
453:
420:
396:
371:
347:
314:
990:
1824:
1781:
1746:
1589:
1579:
1550:
1183:
1176:
912:
652:
575:
566:
558:
330:
387:
1768:
1611:
1571:
1538:
1310:
1296:
1194:
924:
299:
230:
150:
138:
1792:
1658:
1606:
1601:
1114:
919:
830:
692:
24:
1700:
1695:
1648:
1641:
1636:
1621:
1616:
1457:
1392:
1141:
1083:
931:
748:
444:
421:"Integrative and Conjugative Elements (ICEs): What They Do and How They Work"
338:
1705:
1690:
1677:
1429:
1217:
1136:
1131:
1121:
1109:
1048:
850:
541:
315:"Genomic islands: tools of bacterial horizontal gene transfer and evolution"
166:
146:
462:
405:
356:
291:
233:
compared with the rest of the genome. Many genomic islands are flanked by
1736:
1682:
1584:
1528:
1523:
1414:
1375:
1331:
1233:
1038:
974:
860:
624:
520:
222:
210:
142:
283:
1718:
1596:
1380:
1365:
1068:
1043:
870:
246:
1809:
1787:
1484:
1407:
1402:
1167:
1058:
1053:
969:
130:
1291:
1283:
1101:
1063:
715:
242:
1797:
1489:
1030:
994:
493:
18:
16:
Part of a genome that has evidence of horizontal origins
145:. A GI can code for many functions, can be involved in
249:. Some genomic islands, including those adjacent to
1729:
1657:
1570:
1438:
1320:
1309:
1282:
1254:
1204:
1193:
1166:
1155:
1100:
1029:
940:
893:
761:
729:
706:
683:
674:
665:
640:
600:
557:
548:
419:Johnson, Christopher M.; Grossman, Alan D. (2015).
49:. Unsourced material may be challenged and removed.
1006:
505:
8:
1317:
1201:
1163:
1013:
999:
991:
680:
671:
554:
512:
498:
490:
482:at the U.S. National Library of Medicine
452:
395:
346:
109:Learn how and when to remove this message
370:Langille MG, Brinkman FS (March 2009).
262:
7:
251:integrative and conjugative elements
157:(PAIs), while GIs that contain many
47:adding citations to reliable sources
437:10.1146/annurev-genet-112414-055018
225:), their frequent association with
581:Short tandem repeat/Microsatellite
179:Inferring horizontal gene transfer
14:
331:10.1111/j.1574-6976.2008.00136.x
23:
34:needs additional citations for
1667:Last universal common ancestor
1262:Defective interfering particle
585:Trinucleotide repeat disorders
137:. The term is usually used in
1:
1803:Clonally transmissible cancer
1239:Satellite-like nucleic acids
572:Variable number tandem repeat
388:10.1093/bioinformatics/btp030
237:and carry fragments of other
272:Nature Reviews. Microbiology
141:, especially with regard to
1854:
1359:Class II or DNA transposon
1354:Class I or retrotransposon
187:/phylogeny based methods.
176:
159:antibiotic resistant genes
1672:Earliest known life forms
1546:Repeated sequences in DNA
539:
425:Annual Review of Genetics
319:FEMS Microbiology Reviews
219:type IV secretion systems
1519:Endogenous viral element
1337:Horizontal gene transfer
484:Medical Subject Headings
173:Computational prediction
163:horizontal gene transfer
1836:Mobile genetic elements
1216:dsDNA satellite virus (
1774:Helper dependent virus
1090:Biological dark matter
980:Protein tandem repeats
908:Tandemly arrayed genes
1534:Endogenous retrovirus
1507:Origin of replication
1223:ssDNA satellite virus
1213:ssRNA satellite virus
133:that has evidence of
1478:Secondary chromosome
1473:Extrachromosomal DNA
1349:Transposable element
953:Pathogenicity island
195:Comparative genomics
185:comparative genomics
155:pathogenicity island
43:improve this article
1714:Model lipid bilayer
1556:Interspersed repeat
284:10.1038/nrmicro2350
227:tRNA-encoding genes
1024:organic structures
903:Gene amplification
135:horizontal origins
1818:
1817:
1759:Non-cellular life
1566:
1565:
1305:
1304:
1278:
1277:
1232:ssRNA satellite (
988:
987:
889:
888:
757:
756:
661:
660:
550:Repeated sequence
525:repeated sequence
235:repeat structures
119:
118:
111:
93:
1843:
1495:Gene duplication
1318:
1314:self-replication
1202:
1164:
1022:Self-replicating
1015:
1008:
1001:
992:
965:Low copy repeats
958:Symbiosis island
895:Gene duplication
681:
672:
555:
533:gene duplication
514:
507:
500:
491:
467:
466:
456:
416:
410:
409:
399:
367:
361:
360:
350:
310:
304:
303:
267:
229:and a different
114:
107:
103:
100:
94:
92:
58:"Genomic island"
51:
27:
19:
1853:
1852:
1846:
1845:
1844:
1842:
1841:
1840:
1821:
1820:
1819:
1814:
1764:Synthetic virus
1752:Artificial cell
1725:
1653:
1562:
1451:RNA replication
1446:DNA replication
1434:
1425:Group II intron
1323:
1313:
1301:
1292:Mammalian prion
1274:
1250:
1229:dsRNA satellite
1226:ssDNA satellite
1196:
1189:
1158:
1151:
1096:
1025:
1019:
989:
984:
936:
885:
753:
725:
702:
676:Retrotransposon
657:
648:Inverted repeat
636:
621:DNA transposon
617:Retrotransposon
612:Gene conversion
603:
596:
593:
544:
535:
518:
480:Genomic+islands
476:
471:
470:
418:
417:
413:
369:
368:
364:
312:
311:
307:
269:
268:
264:
259:
239:mobile elements
207:
181:
175:
129:) is part of a
115:
104:
98:
95:
52:
50:
40:
28:
17:
12:
11:
5:
1851:
1850:
1847:
1839:
1838:
1833:
1823:
1822:
1816:
1815:
1813:
1812:
1807:
1806:
1805:
1800:
1790:
1784:
1778:
1777:
1776:
1771:
1761:
1756:
1755:
1754:
1749:
1739:
1733:
1731:
1727:
1726:
1724:
1723:
1722:
1721:
1716:
1708:
1703:
1698:
1693:
1687:
1686:
1685:
1674:
1669:
1663:
1661:
1655:
1654:
1652:
1651:
1646:
1645:
1644:
1639:
1631:
1629:Kappa organism
1626:
1625:
1624:
1619:
1614:
1609:
1604:
1594:
1593:
1592:
1587:
1576:
1574:
1568:
1567:
1564:
1563:
1561:
1560:
1559:
1558:
1553:
1543:
1542:
1541:
1536:
1531:
1526:
1516:
1515:
1514:
1504:
1503:
1502:
1500:Non-coding DNA
1497:
1492:
1482:
1481:
1480:
1475:
1470:
1465:
1455:
1454:
1453:
1442:
1440:
1436:
1435:
1433:
1432:
1427:
1422:
1420:Group I intron
1417:
1412:
1411:
1410:
1400:
1399:
1398:
1395:
1386:
1383:
1378:
1373:
1363:
1362:
1361:
1356:
1346:
1345:
1344:
1342:Genomic island
1339:
1328:
1326:
1322:Mobile genetic
1315:
1307:
1306:
1303:
1302:
1300:
1299:
1294:
1288:
1286:
1280:
1279:
1276:
1275:
1273:
1272:
1271:
1270:
1267:
1258:
1256:
1252:
1251:
1249:
1248:
1247:
1246:
1243:
1237:
1230:
1227:
1224:
1221:
1214:
1210:
1208:
1199:
1191:
1190:
1188:
1187:
1180:
1172:
1170:
1161:
1153:
1152:
1150:
1149:
1147:dsDNA-RT virus
1144:
1142:ssRNA-RT virus
1139:
1137:(−)ssRNA virus
1134:
1132:(+)ssRNA virus
1129:
1124:
1119:
1118:
1117:
1106:
1104:
1098:
1097:
1095:
1094:
1093:
1092:
1087:
1077:Incertae sedis
1073:
1072:
1071:
1066:
1061:
1056:
1046:
1041:
1035:
1033:
1027:
1026:
1020:
1018:
1017:
1010:
1003:
995:
986:
985:
983:
982:
977:
972:
967:
962:
961:
960:
955:
948:Genomic island
944:
942:
938:
937:
935:
934:
929:
928:
927:
917:
916:
915:
905:
899:
897:
891:
890:
887:
886:
884:
883:
878:
873:
868:
863:
858:
853:
848:
843:
838:
833:
828:
823:
818:
813:
808:
803:
798:
793:
788:
783:
778:
773:
767:
765:
763:DNA transposon
759:
758:
755:
754:
752:
751:
746:
741:
735:
733:
727:
726:
724:
723:
718:
712:
710:
704:
703:
701:
700:
695:
689:
687:
678:
669:
663:
662:
659:
658:
656:
655:
650:
644:
642:
638:
637:
635:
634:
633:
632:
627:
619:
614:
608:
606:
598:
597:
595:
594:
591:Macrosatellite
588:
578:
569:
563:
561:
559:Tandem repeats
552:
546:
545:
540:
537:
536:
519:
517:
516:
509:
502:
494:
488:
487:
475:
474:External links
472:
469:
468:
411:
376:Bioinformatics
362:
325:(2): 376–393.
305:
261:
260:
258:
255:
206:
203:
177:Main article:
174:
171:
123:genomic island
117:
116:
99:September 2011
31:
29:
22:
15:
13:
10:
9:
6:
4:
3:
2:
1849:
1848:
1837:
1834:
1832:
1829:
1828:
1826:
1811:
1808:
1804:
1801:
1799:
1796:
1795:
1794:
1791:
1789:
1785:
1783:
1782:Nanobacterium
1779:
1775:
1772:
1770:
1767:
1766:
1765:
1762:
1760:
1757:
1753:
1750:
1748:
1747:Cell division
1745:
1744:
1743:
1740:
1738:
1735:
1734:
1732:
1728:
1720:
1717:
1715:
1712:
1711:
1709:
1707:
1704:
1702:
1699:
1697:
1694:
1692:
1688:
1684:
1681:
1680:
1679:
1675:
1673:
1670:
1668:
1665:
1664:
1662:
1660:
1656:
1650:
1647:
1643:
1640:
1638:
1635:
1634:
1632:
1630:
1627:
1623:
1620:
1618:
1615:
1613:
1610:
1608:
1605:
1603:
1600:
1599:
1598:
1595:
1591:
1590:Hydrogenosome
1588:
1586:
1583:
1582:
1581:
1580:Mitochondrion
1578:
1577:
1575:
1573:
1572:Endosymbiosis
1569:
1557:
1554:
1552:
1551:Tandem repeat
1549:
1548:
1547:
1544:
1540:
1537:
1535:
1532:
1530:
1527:
1525:
1522:
1521:
1520:
1517:
1513:
1510:
1509:
1508:
1505:
1501:
1498:
1496:
1493:
1491:
1488:
1487:
1486:
1483:
1479:
1476:
1474:
1471:
1469:
1466:
1464:
1461:
1460:
1459:
1456:
1452:
1449:
1448:
1447:
1444:
1443:
1441:
1439:Other aspects
1437:
1431:
1428:
1426:
1423:
1421:
1418:
1416:
1413:
1409:
1406:
1405:
1404:
1401:
1396:
1394:
1390:
1387:
1384:
1382:
1379:
1377:
1374:
1372:
1369:
1368:
1367:
1364:
1360:
1357:
1355:
1352:
1351:
1350:
1347:
1343:
1340:
1338:
1335:
1334:
1333:
1330:
1329:
1327:
1325:
1319:
1316:
1312:
1308:
1298:
1295:
1293:
1290:
1289:
1287:
1285:
1281:
1268:
1265:
1264:
1263:
1260:
1259:
1257:
1253:
1244:
1241:
1240:
1238:
1235:
1231:
1228:
1225:
1222:
1219:
1215:
1212:
1211:
1209:
1207:
1203:
1200:
1198:
1192:
1186:
1185:
1184:Avsunviroidae
1181:
1179:
1178:
1177:Pospiviroidae
1174:
1173:
1171:
1169:
1165:
1162:
1160:
1154:
1148:
1145:
1143:
1140:
1138:
1135:
1133:
1130:
1128:
1125:
1123:
1120:
1116:
1113:
1112:
1111:
1108:
1107:
1105:
1103:
1099:
1091:
1088:
1086:
1085:
1081:
1080:
1079:
1078:
1074:
1070:
1067:
1065:
1062:
1060:
1057:
1055:
1052:
1051:
1050:
1047:
1045:
1042:
1040:
1037:
1036:
1034:
1032:
1031:Cellular life
1028:
1023:
1016:
1011:
1009:
1004:
1002:
997:
996:
993:
981:
978:
976:
973:
971:
968:
966:
963:
959:
956:
954:
951:
950:
949:
946:
945:
943:
939:
933:
930:
926:
923:
922:
921:
918:
914:
913:Ribosomal DNA
911:
910:
909:
906:
904:
901:
900:
898:
896:
892:
882:
879:
877:
874:
872:
869:
867:
864:
862:
859:
857:
854:
852:
849:
847:
844:
842:
839:
837:
834:
832:
829:
827:
824:
822:
819:
817:
814:
812:
809:
807:
804:
802:
799:
797:
794:
792:
789:
787:
784:
782:
779:
777:
774:
772:
769:
768:
766:
764:
760:
750:
747:
745:
742:
740:
737:
736:
734:
732:
728:
722:
719:
717:
714:
713:
711:
709:
705:
699:
696:
694:
691:
690:
688:
686:
682:
679:
677:
673:
670:
668:
664:
654:
653:Direct repeat
651:
649:
646:
645:
643:
639:
631:
628:
626:
623:
622:
620:
618:
615:
613:
610:
609:
607:
605:
599:
592:
589:
586:
582:
579:
577:
576:Minisatellite
573:
570:
568:
567:Satellite DNA
565:
564:
562:
560:
556:
553:
551:
547:
543:
538:
534:
530:
526:
522:
515:
510:
508:
503:
501:
496:
495:
492:
485:
481:
478:
477:
473:
464:
460:
455:
450:
446:
442:
438:
434:
430:
426:
422:
415:
412:
407:
403:
398:
393:
389:
385:
381:
377:
373:
366:
363:
358:
354:
349:
344:
340:
336:
332:
328:
324:
320:
316:
309:
306:
301:
297:
293:
289:
285:
281:
278:(5): 373–82.
277:
273:
266:
263:
256:
254:
252:
248:
244:
240:
236:
232:
228:
224:
220:
216:
212:
204:
202:
199:
196:
192:
188:
186:
180:
172:
170:
168:
164:
160:
156:
152:
148:
144:
140:
136:
132:
128:
124:
113:
110:
102:
91:
88:
84:
81:
77:
74:
70:
67:
63:
60: –
59:
55:
54:Find sources:
48:
44:
38:
37:
32:This article
30:
26:
21:
20:
1831:Cell biology
1769:Viral vector
1612:Gerontoplast
1539:Transpoviron
1341:
1311:Nucleic acid
1297:Fungal prion
1195:Helper-virus
1182:
1175:
1082:
1075:
947:
925:Gene cluster
693:Alu sequence
602:Interspersed
428:
424:
414:
382:(5): 664–5.
379:
375:
365:
322:
318:
308:
275:
271:
265:
208:
200:
193:
189:
182:
151:pathogenesis
139:microbiology
126:
122:
120:
105:
96:
86:
79:
72:
65:
53:
41:Please help
36:verification
33:
1793:Cancer cell
1659:Abiogenesis
1607:Chromoplast
1602:Chloroplast
1385:Degradative
1127:dsRNA virus
1122:ssDNA virus
1115:Giant virus
1110:dsDNA virus
920:Gene family
831:Tc1/mariner
786:EnSpm/CACTA
431:: 577–601.
231:G+C content
1825:Categories
1701:Proteinoid
1696:Coacervate
1649:Nitroplast
1642:Trophosome
1637:Bacteriome
1622:Apicoplast
1617:Leucoplast
1458:Chromosome
1376:Resistance
1084:Parakaryon
932:Pseudogene
749:retroposon
667:Transposon
529:transposon
257:References
69:newspapers
1710:Research
1691:Protocell
1430:Retrozyme
1389:Virulence
1371:Fertility
1218:Virophage
1206:Satellite
1197:dependent
1049:Eukaryota
851:P element
801:Harbinger
542:Repeatome
445:0066-4197
339:0168-6445
167:phylogeny
147:symbiosis
1737:Organism
1730:See also
1706:Sulphobe
1683:Ribozyme
1678:RNA life
1585:Mitosome
1529:Prophage
1524:Provirus
1512:Replicon
1468:Circular
1415:Phagemid
1332:Mobilome
1324:elements
1234:Virusoid
1157:Subviral
1069:Protista
1054:Animalia
1039:Bacteria
975:Telomere
941:See also
881:Zisupton
861:Polinton
856:PiggyBac
811:Helitron
630:Helitron
625:Polinton
521:Genetics
463:26473380
406:19151094
357:19178566
292:20395967
247:plasmids
241:such as
215:type III
211:bacteria
205:Examples
143:bacteria
1719:Jeewanu
1633:Organs
1597:Plastid
1397:Cryptic
1366:Plasmid
1064:Plantae
1044:Archaea
871:Transib
846:Novosib
826:Kolobok
796:Ginger2
791:Ginger1
776:Crypton
454:5180612
397:2647836
348:2704930
300:2373228
213:, many
83:scholar
1810:Virome
1788:Nanobe
1485:Genome
1463:Linear
1408:Fosmid
1403:Cosmid
1168:Viroid
1159:agents
970:CRISPR
836:Merlin
821:ISL2EU
771:Academ
604:repeat
486:(MeSH)
461:
451:
443:
404:
394:
355:
345:
337:
298:
290:
243:phages
131:genome
85:
78:
71:
64:
56:
1284:Prion
1255:Other
1102:Virus
1059:Fungi
876:Zator
816:IS3EU
721:LINE2
716:LINE1
708:LINEs
685:SINEs
641:Other
296:S2CID
90:JSTOR
76:books
1798:HeLa
1742:Cell
1490:Gene
866:Sola
841:MuDR
781:Dada
744:MER4
739:HERV
731:LTRs
459:PMID
441:ISSN
402:PMID
353:PMID
335:ISSN
288:PMID
245:and
217:and
62:news
1381:Col
1269:DNA
1266:RNA
1245:DNA
1242:RNA
806:hAT
698:MIR
449:PMC
433:doi
392:PMC
384:doi
343:PMC
327:doi
280:doi
209:In
149:or
45:by
1827::
1393:Ti
531:,
527:,
523::
457:.
447:.
439:.
429:49
427:.
423:.
400:.
390:.
380:25
378:.
374:.
351:.
341:.
333:.
323:33
321:.
317:.
294:.
286:.
274:.
223:Kb
127:GI
121:A
1786:?
1780:?
1689:†
1676:?
1391:/
1236:)
1220:)
1014:e
1007:t
1000:v
587:)
583:(
574:/
513:e
506:t
499:v
465:.
435::
408:.
386::
359:.
329::
302:.
282::
276:8
125:(
112:)
106:(
101:)
97:(
87:·
80:·
73:·
66:·
39:.
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
