Research

Comparative genomics

With the availability of whole genome sequences of multiple Arthrospira as well as other Cyanobacteria species, we are interested in applying comparative genomics to study the genomic diversity among various micro-algae. We are particularly interested in identifying variations in gene contents that may introduce new metabolic capacities. We are developing an algorithm that allows us to compare the gene contents found in multiple  draft and complete genomes as shown in Figure 1.

Figure 1. An overview of our method for comparing gene contents found in multiple draft and complete genomes

Our method has been used to analyze the gene content form 100 Cyanobacteria genomes as listed in Table 1. This allows us to characterize the core as well as variable gene pools of Arthrospira as well as other Cyanobacteria species. We are currently analyzing the variations in gene contents with respect to metabolic capacities. Result from this may allow us to introduce new biosynthetic pathways from one Cyanobacteria species to other.

 

Table 1. 100 Cyanobacterial genomes used in our comparative genomics study

Organism_name Number of genes Genome size (Mbp) Number of Coding sequences Number of Contigs/ Scaffold
Acaryochloris marina MBIC11017 6329 6503.724 6254 1
Anabaena cylindrica PCC 7122 5393 6395.836 5320 1
Anabaena sp. 90 4570 5305.675 4511 5
Anabaena variabilis ATCC 29413 5102 6365.727 5043 1
Arthrospira maxima CS-328 5728 6003.314 5690 129
Arthrospira platensis C1 6153 6089.21 6108 1
Arthrospira platensis NIES-39 6676 6788.435 6630 1
Calothrix sp. PCC 6303 5446 6767.834 5393 1
Calothrix sp. PCC 7507 6031 7023.215 5950 1
Chamaesiphon minutus PCC 6605 5561 6284.095 5498 1
Chroococcidiopsis thermalis PCC 7203 5463 6315.792 5408 1
Crinalium epipsammum PCC 9333 4529 5315.554 4474 1
Crocosphaera watsonii WH 8501 5996 6238.156 5958 323
Cyanobacterium aponinum PCC 10605 3410 4114.099 3358 1
Cyanobacterium stanieri PCC 7202 2889 3163.381 2837 1
cyanobacterium UCYN-A 1241 1443.806 1199 1
Cyanobium gracile PCC 6307 3330 3342.364 3280 1
Cyanothece sp. ATCC 51142 4813 4934.271 4762 1
Cyanothece sp. ATCC 51472 5126 5428.187 5083 48
Cyanothece sp. PCC 7424 5280 5942.652 5227 1
Cyanothece sp. PCC 7425 5019 5374.574 4966 1
Cyanothece sp. PCC 7822 5478 6091.62 5422 1
Cyanothece sp. PCC 8801 4309 4679.413 4260 1
Cyanothece sp. PCC 8802 4368 4669.813 4320 1
Cylindrospermopsis raciborskii CS-505 3500 3879.03 3449 93
Cylindrospermum stagnale PCC 7417 5892 7003.56 5811 1
Dactylococcopsis salina PCC 8305 3388 3781.008 3337 1
Fischerella sp. JSC-11 4671 5380 4627 34
Geitlerinema sp. PCC 7407 3870 4681.111 3815 1
Gloeobacter violaceus PCC 7421 4478 4659.019 4430 1
Halothece sp. PCC 7418 3763 4179.17 3708 1
Leptolyngbya sp. PCC 6406 5236 5606.57 5190 377
Leptolyngbya sp. PCC 7375 7900 9422.968 7828 5
Leptolyngbya sp. PCC 7376 4278 5125.95 4228 1
Lyngbya aestuarii BL J 6568 6873.508 6515 439
Lyngbya sp. PCC 8106 6185 7037.511 6142 110
Microcoleus sp. PCC 7113 6106 7470.429 6027 1
Microcoleus vaginatus FGP-2 5209 6698.929 5134 40
Microcystis aeruginosa NIES-843 6360 5842.795 6312 1
Microcystis aeruginosa PCC 7941 4563 4801.899 4520 77
Microcystis aeruginosa PCC 9432 4803 4994.942 4760 132
Microcystis aeruginosa PCC 9443 4824 5185.041 4780 221
Microcystis aeruginosa PCC 9701 4527 4755.998 4483 323
Microcystis aeruginosa PCC 9717 4880 5300.338 4836 264
Microcystis aeruginosa PCC 9806 4038 4262.564 3994 93
Microcystis aeruginosa PCC 9807 4828 5155.707 4784 267
Microcystis aeruginosa PCC 9808 4888 5051.045 4845 141
Microcystis aeruginosa PCC 9809 4724 5011.016 4680 303
Microcystis aeruginosa SPC 777 5289 5454.996 5241 278
Microcystis aeruginosa TAIHU98 5404 4849.611 5356 4
Microcystis sp. T1-4 4478 4693.747 4434 449
Nodularia spumigena CCY9414 4904 5316.258 4860 204
Nostoc punctiforme PCC 73102 6186 8234.322 6086 1
Nostoc sp. PCC 7107 5327 6329.823 5237 1
Nostoc sp. PCC 7120 5425 6413.771 5365 1
Nostoc sp. PCC 7524 5415 6635.03 5355 1
Oscillatoria acuminata PCC 6304 5779 7689.443 5704 1
Oscillatoria nigro-viridis PCC 7112 5859 7479.014 5781 1
Oscillatoria sp. PCC 6506 5891 6676.705 5822 377
Oscillatoriales cyanobacterium JSC-12 4831 5530.491 4780 1
Pleurocapsa sp. PCC 7327 4319 4986.817 4268 1
Prochlorococcus marinus str. AS9601 1961 1669.886 1920 1
Prochlorococcus marinus str. MIT 9211 1897 1688.963 1854 1
Prochlorococcus marinus str. MIT 9215 2021 1738.79 1982 1
Prochlorococcus marinus str. MIT 9301 1946 1641.879 1906 1
Prochlorococcus marinus str. MIT 9303 3046 2682.675 2997 1
Prochlorococcus marinus str. MIT 9312 1852 1709.204 1810 1
Prochlorococcus marinus str. MIT 9313 2321 2410.873 2269 1
Prochlorococcus marinus str. MIT 9515 1945 1704.176 1905 1
Prochlorococcus marinus str. NATL1A 2234 1864.731 2193 1
Prochlorococcus marinus str. NATL2A 2203 1842.899 2162 1
Pseudanabaena biceps PCC 7429 4803 5476.421 4757 464
Pseudanabaena sp. PCC 7367 3613 4557.046 3561 1
Raphidiopsis brookii D9 3057 3186.511 3007 47
Rivularia sp. PCC 7116 6670 8698.463 6609 1
Rubidibacter lacunae KORDI 51-2 3501 4153.658 3457 99
Stanieria cyanosphaera PCC 7437 4377 5041.209 4328 1
Synechococcus elongatus PCC 6301 2574 2696.255 2523 1
Synechococcus elongatus PCC 7942 2662 2695.903 2612 1
Synechococcus sp. BL107 2553 2285.034 2507 1
Synechococcus sp. CC9311 2942 2606.748 2892 1
Synechococcus sp. CC9605 2696 2510.659 2645 1
Synechococcus sp. CC9902 2357 2234.828 2306 1
Synechococcus sp. JA-3-3Ab 2813 2932.766 2760 1
Synechococcus sp. PCC 6312 3557 3697.276 3513 1
Synechococcus sp. PCC 7002 2872 3008.047 2824 1
Synechococcus sp. PCC 7502 3297 3510.253 3248 1
Synechococcus sp. RCC307 2579 2224.914 2534 1
Synechococcus sp. RS9916 3009 2664.873 2961 1
Synechococcus sp. RS9917 2820 2584.918 2770 1
Synechococcus sp. WH 5701 3401 3280.236 3346 116
Synechococcus sp. WH 7803 2583 2366.98 2533 1
Synechococcus sp. WH 8016 3037 2694.843 2992 16
Synechococcus sp. WH 8102 2569 2434.428 2519 1
Synechocystis sp. PCC 6803 3207 3569.561 3159 1
Synechocystis sp. PCC 6803 substr. PCC-N 3216 3570.103 3168 1
Synechocystis sp. PCC 6803 substr. PCC-P 3216 3570.114 3168 1
Thermosynechococcus elongatus BP-1 2521 2593.857 2476 1
Trichodesmium erythraeum IMS101 4494 7750.108 4451 1
Xenococcus sp. PCC 7305 5414 5929.641 5373 234

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