Table 2 |
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|
Chromosomal locations of duplications and their distribution among strains |
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| Duplication |
Chromosome |
Start (gene) |
Start (position) |
Stop (gene) |
Stop (position) |
Length, bp (estimated) |
Strain |
|
|
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| 1A |
1 |
DDB0216544 |
597,838 |
DDB0202121 |
630,646 |
32,808 |
NP81, HU32 |
| 1B |
1 |
DDB0190413 |
3,180,718 |
DDB0190424 |
3,207,169 |
26,451 |
Ax2(all) |
| 1C |
1 |
DDB0190683 |
3,902,919 |
DDB0190710 |
3,958,366 |
55,447 |
KAx3(U) |
| 1D |
1 |
DDB0190972 |
4,651,366 |
end |
4,923,596 |
272,230 |
Ax2(I) |
| 2A |
2 |
end |
1 |
DDB0216807 |
200,951 |
200,950 |
NP81 |
| 2B |
2 |
DDB0217042 |
1,829,463 |
DDB0167938 |
3,760,461 |
1,930,998 |
Ax2(Wee) |
| 2C |
2 |
DDB0168867 |
1,848,568 |
DDB0217158 |
3,002,504 |
1,153,936 |
Ax2-214 |
| 2D |
2 |
DDB0168894 |
1,898,568 |
DDB0231868 |
3,020,328 |
1,121,760 |
Ax2(M) |
| 2E |
2 |
DDB0185119 |
2,249,563 |
DDB0217157 |
3,002,134 |
752,571 |
Ax3/Ax4(all), NC4A2(both), JH10, DH1, HU32, NP81 |
| 2F |
2 |
DDB0203552 |
6,131,391 |
DDB0217791 |
6,752,329 |
620,938 |
Ax2-206 |
| 2G |
2 |
DDB0169405 |
6,623,914 |
DDB0217791 |
6,752,329 |
128,415 |
JH10 |
| 2H |
2 |
DDB0217974 |
7,981,227 |
end |
8,470,628 |
489,401 |
NC4(L), NC4(Kn) |
| 2I |
2 |
DDB0203385 |
8,080,299 |
DDB0217992 |
8,181,086 |
100,787 |
DH1, Ax3(D) |
| 3A |
3 |
DDB0206361 |
2,898,815 |
DDB0206368 |
2,915,972 |
17,157 |
NP81, HU32 |
| 3B |
3 |
DDB0206089 |
3,595,775 |
DDB0206091 |
3,599,648 |
3,873 |
all non-NC4, some NC4s, X22 |
| 4A |
4 |
DDB0186951 |
4,413,680 |
DDB0186970 |
4,474,299 |
60,619 |
NC28.2 |
| 4B |
4 |
DDB0218826 |
4,572,845 |
end |
5,450,249 |
877,404 |
NC4(B) |
| 5A |
5 |
DDB0219507 |
3,476,579 |
DDB0188678 |
3,531,501 |
54,922 |
DH1, Ax3(C), Ax3(D), Ax4(F), XP99, HU32, NP81 |
| 6A |
6 |
DDB0183998 |
578,375 |
DDB0184007 |
595,296 |
16,921 |
NP81, HU32 |
| 6B |
6 |
DDB0184069 |
763,797 |
DDB0184181 |
1,066,872 |
303,075 |
XP99 |
| 6C |
6 |
DDB0219696 |
767,768 |
DDB0219699 |
787,282 |
19,514 |
NP81, HU32 |
| 6D |
6 |
DDB0191606 |
838,926 |
DDB0184104 |
858,379 |
19,453 |
NP81, HU32 |
| 6E |
6 |
DDB0184203 |
1,144,841 |
end |
3,602,379 |
2,457,538 |
Ax2-206 |
| 6F |
6 |
DDB0184511 |
1,919,891 |
DDB0219875 |
3,055,147 |
1,135,256 |
Ax2-206 |
| 6G |
6 |
DDB0191998 |
3,022,031 |
DDB0219875 |
3,055,147 |
33,116 |
NP81, HU32 |
| 6H |
6 |
DDB0192115 |
3,311,430 |
end |
3,602,379 |
290,949 |
NC4(Wi) |
| 6I |
6 |
DDB0192193 |
3,468,862 |
end |
3,602,379 |
133,517 |
NC4(S) |
|
|
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|
Breakpoints were estimated by eye, and their map locations determined by aligning the probe sequence with the dictyBase assembly version 2.5. The duplication in the sequenced strain is given as the breakpoints and size revealed by the sequence itself. As noted in the text there appears to be variation in this duplication among the different strains that inherited it. The putative duplications in Ax2-214 and Ax2(M) are atypical in that the average log2 ratio across their lengths is considerably lower than 0.5. The larger duplication of chromosome 6 sequence in Ax2-206 may be similar in this respect. We do not understand why these features differ from the more typical duplications we observe. |
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|
Bloomfield et al. Genome Biology 2008 9:R75 doi:10.1186/gb-2008-9-4-r75 |
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