Background
Methods
Mosquito strains and chromosome preparation
Fluorescence in situ hybridization
Gene orthology, syntenic blocks and fixed inversion
Chromosome evolution in Anopheles mosquitoes
Results
A physical genome map of Anopheles sinensis
Clone name on the map | Scaffold name | Chromosome location in An. sinensis
| Length (bp) | |
---|---|---|---|---|
1 | 695491 | AS2_scf7180000695491 | X:1A | 730,280 |
2 | 695557 | AS2_scf7180000695557 | X:1A_B | 1,255,381 |
3 | 695865 | AS2_scf7180000695865 | X:1B_C | 2,684,564 |
4 | 695541 | AS2_scf7180000695541 | X:1C_2A | 841,721 |
5 | 696079 | AS2_scf7180000696079 | X:2A_B | 2,239,752 |
6 | 695680 | AS2_scf7180000695680 | X:2B_3A | 1,772,387 |
7 | 696050 | AS2_scf7180000696050 | X:3A_4A | 2,422,445 |
8 | 695709 | AS2_scf7180000695709 | X:4A_5A | 1,472,510 |
9 | 695705 | AS2_scf7180000695705 | 2R:6C | 3,132,144 |
10 | 695681 | AS2_scf7180000695681 | 2R:7B | 3,622,691 |
11 | 696027 | AS2_scf7180000696027 | 2R:8A | 1,402,797 |
12 | 696017 | AS2_scf7180000696017 | 2R:8B | 401,984 |
13 | 696051 | AS2_scf7180000696051 | 2R:9B | 1,646,812 |
14 | 696133 | AS2_scf7180000696133 | 2R:9B_10A | 2,071,771 |
15 | 696054 | AS2_scf7180000696054 | 2R:10C_11A | 2,075,225 |
16 | 696041 | AS2_scf7180000696041 | 2R:11B | 1,460,364 |
17 | 695763 | AS2_scf7180000695763 | 2R:11C_12A | 1,569,060 |
18 | 696013 | AS2_scf7180000696013 | 2R:13A | 1,443,628 |
19 | 695690 | AS2_scf7180000695690 | 2R:14A_B | 1,623,961 |
20 | 696012 | AS2_scf7180000696012 | 2R:14C_D | 1,036,301 |
21 | 696047 | AS2_scf7180000696047 | 2L:17A_B | 1,804,022 |
22 | 696045 | AS2_scf7180000696045 | 2L:18A | 1,433,044 |
23 | 696048 | AS2_scf7180000696048 | 2L:18B | 1,655,828 |
24 | 696056 | AS2_scf7180000696056 | 2L:18C | 2,410,210 |
25 | 695983 | AS2_scf7180000695983 | 2:19B | 1,798,621 |
26 | 696058 | AS2_scf7180000696058 | 2L:20A | 2,460,545 |
27 | 696057 | AS2_scf7180000696057 | 2L:20D | 3,056,258 |
28 | 696060 | AS2_scf7180000696060 | 2L:22C_23B | 4,138,565 |
29 | 695970 | AS2_scf7180000695970 | 3R:24A_B | 1,982,586 |
30 | 695742 | AS2_scf7180000695742 | 3R:24B_25A | 1,869,526 |
31 | 695544 | AS2_scf7180000695544 | 3R:25A_B | 1,280,009 |
32 | 696022 | AS2_scf7180000696022 | 3R:27B_C | 621,276 |
33 | 694399 | AS2_scf7180000694399 | 3R:28B | 146,261 |
34 | 695645 | AS2_scf7180000695645 | 3R:29B | 17,918 |
35 | 695987 | AS2_scf7180000695987 | 3R:30A | 525,874 |
36 | 687438 | AS2_scf7180000697438 | 3R:30A | 140,738 |
37 | 696078 | AS2_scf7180000696078 | 3R:31A | 229,900 |
38 | 691904 | AS2_scf7180000691904 | 3R:31A | 138,869 |
39 | 695864 | AS2_scf7180000695864 | 3R:32A | 170,159 |
40 | 696020 | AS2_scf7180000696020 | 3R:32A | 710,710 |
41 | 696131 | AS2_scf7180000696131 | 3R:32B | 2,359,367 |
42 | 695941 | AS2_scf7180000695941 | 3R:32C | 816,509 |
43 | 696018 | AS2_scf7180000696018 | 3L:33A | 515,011 |
44 | 696001 | AS2_scf7180000696001 | 3L:34C | 777,379 |
45 | 695556 | AS2_scf7180000695556 | 3L:34C_D | 1,591,401 |
46 | 696053 | AS2_scf7180000696053 | 3L:35A | 1,670,191 |
47 | 695549 | AS2_scf7180000695549 | 3L:37A | 814,231 |
48 | 696039 | AS2_scf7180000696039 | 3L:37A | 3,601,930 |
49 | 695747 | AS2_scf7180000695747 | 3L:37C | 566,275 |
50 | 696026 | AS2_scf7180000696026 | 3L:37C_38A | 1,091,046 |
51 | 696059 | AS2_scf7180000696059 | 3L:38B | 2,208,365 |
52 | 696055 | AS2_scf7180000696055 | 3L:38C_39C | 5,918,260 |
Chromosome arm | Scaffolds mapped (n) | Length (bp) | Total sequenced genome (%) |
---|---|---|---|
X | 8 | 13,419,040 | 6.07 |
2R | 12 | 17,382,848 | 7.87 |
2L | 8 | 18,757,093 | 8.50 |
3R | 14 | 11,009,702 | 4.99 |
3L | 10 | 18,754,089 | 8.49 |
Total | 52 | 79,322,772 | 36.00 |
Species | Genome assembly | Total scaffolds | Mapped scaffolds | Scaffold N50, bp | Total length, Mb | Mapped length, Mb | Mapped, % |
---|---|---|---|---|---|---|---|
An. albimanus
| AalbS1 | 204 | 40 | 18,068,499 | 170.5 | 167.4 | 98.2 |
An. gambiae
| AgamP4 | 8 | 5 | 49,364,325 | 264 | 273.1 | 84.3 |
An. stephensi
| AsteI2 | 23,371 | 86 | 1,591,355 | 221.3 | 137.14 | 62 |
An. stephensi
| AsteS1 | 1100 | 101 | 837,295 | 225 | 92.83 | 41 |
An. atroparvus
| AatrE1 | 1371 | 7 | 9,206,694 | 224.3 | 88.8 | 39.6 |
An. sinensis
| AsinC2 | 9592 | 52 | 814,231 | 220.8 | 79.3 | 35.9 |
An. funestus
| AfunF1 | 1392 | 103 | 671,960 | 225.2 | 79.0 | 35.1 |
Synteny and gene order evolution in An. sinensis and An. gambiae
Chromosome | Number of synteny blocks (n) | The average length of synteny blocks (bp) | The largest synteny blocks (bp) | The smallest synteny blocks (bp) |
---|---|---|---|---|
X | 112 | 85,989 | 766,489 | 1676 |
2R | 68 | 237,175 | 1,796,395 | 1796 |
2L | 70 | 239,627 | 1,629,455 | 1514 |
3R | 47 | 197,751 | 1,709,848 | 3361 |
3L | 67 | 242,299 | 1,469,290 | 4748 |
Total | 364 | 191,358 | 1,474,295 | 2619 |
Chromosome name in An. sinensis
| Size of mapped scaffolds in An. sinensis (Mb) | Inversions (GRIMM) | Inversions/Mb | Inversions/Mb/MY (divergence time 58 MY) |
---|---|---|---|---|
X | 13.419 | 101 | 7.527 | 0.130 |
2R | 17.382 | 42 | 2.416 | 0.042 |
2L | 18.757 | 51 | 2.719 | 0.047 |
3R | 11.010 | 33 | 2.997 | 0.052 |
3L | 18.754 | 40 | 2.133 | 0.037 |
Total | 79.322 | 267 | 3.366 | 0.058 |
Rapid evolution of the sex chromosome in Anopheles mosquitoes
Species | X | 2R | 2L | 3R | 3L |
---|---|---|---|---|---|
An. albimanus–An. gambiae
| 0.130 | 0.043 | 0.040 | 0.034 | 0.037 |
An. atroparvus–An. gambiae
| 0.124 | 0.036 | 0.035 | 0.025 | 0.041 |
An. funestus–An. gambiae
| 0.121 | 0.064 | 0.065 | 0.026 | 0.066 |
An. sinensis–An. gambiae
| 0.130 | 0.052 | 0.047 | 0.042 | 0.037 |
An. stephensi–An. gambiae
| 0.128 | 0.049 | 0.036 | 0.028 | 0.036 |