Department of Protozoology
 Nagasaki Univ   Institute of Tropical Medicine Department of Protozoology Kaneko Pf Basic
P. FALCIPARUM BASIC VALUES
Compiled by Osamu Kaneko, (Dec/16/2009 update)
genome P. falciparum genome and other organisms [Gardner et al Nature 419. 2002 Table 1, partial]
  P. falciparum S. pombe S. cerevisiae D. discoideum A. thaliana
size 22,853,764 12,462,637 12,495,682 8,100,000 115,409,949
(G+C) content 19.4% 36.0% 38.3% 22.2% 34.9%
No of genes 5,268 4,929 5,770 2,799 25,498
Mean gene length 2,283 bp 1,426 bp 1,424 bp 1,626 bp 1,310 bp
Genes with intron 53.9% 43% 5.0% 68% 79%
Exons
  number 12,674 nd nd 6,398 132,982
  No. per gene 2.39 nd na 2.29 5.18
  GC content 23.7% 39.6% 28.0% 28.0% nd
  Mean length 949 bp nd nd 711 bp 170 bp
Introns
  number 7,406 4,730 272 3,587 107,784
  (G+C) content 13.5 nd na 13.0 nd
  Mean length (bp) 178.7 81 na 177 170
Intergenic regions
  (G+C) content 13.6 nd nd 14.0 nd
  Mean length (bp) 1,694 952 515 786 nd
RNAs
  # of tRNA 43 174 nd 73 nd
  # of 5S rRNA 3 30 nd na nd
  # of 5.8S, 18S, 28S
    rRNA unit		 7 200-400 nd na 700-800

ND, not determined.  NA, not available.  "# of genes" for D. discoideum are for chr 2.

S. pombe [Wood V et al. The genome sequence of S. pombe. Nature 415 (2002)]
S. cerevisiae [Wood V et al. A re-annotation of the S. cerevisiae genome. Comp Funct Genom 2 (2001)]
D. discoideum[Glockner G et al. Sequence and analysis of chromosome 2 of D. discoideum. Nature 418 (2002)]
A. thaliana [Analysis of the genome sequence of the flowering plant A. thaliana. Nature 408 (2000)]
SNPs Polymorphism in 204 genes of chromosome 3 [Mu et al. Nature 418, 2002 Table 2]
Polymorphism No. of bp
screened		 No. of
polys		 SNP/bp Theta (x10-4)
(mean +/- s.e.)		 Pi (x10-4)
(mean +/- s.e.)
Total SNPs 218,152 238 1/917 5.2 4.9
Non-coding 16,083 31 1/519 10.3+/- 1.77 9.4 +/- 0.85
Coding 202,069 207 1/976 4.8 +/- 0.59 4.4 +/- 0.57
Syn 38,480 62 1/620 7.2 +/- 1.04 6.8 +/- 0.97
Nsyn 163,498 145 1/1,128 4.2 +/- 0.71 3.9 +/- 0.55
Microsatellite 218,152 165 1/1,299

Polymorphism in 3539 (among 5401) genes of all 14 chromosomes [Mu et al. Nature Genetics 39, 2007 Table 1]
Polymorphism No. of bp
screened		 No. of
polys		 SNP/bp Theta (x10-4)
(mean +/- s.e.)		 Pi (x10-4)
(mean +/- s.e.)
Total SNPs 4,249,816 3918   4.83 5.05
Non-coding   208      
Coding   3,710      
Syn   1,150      
Nsyn   2,560      
Microsatellite   2,548  

Data from 5 P. falciparum lines (3D7, Dd2, HB3, 7G8, and D10).
Theta, nucleotide polymorphism; Pi, nucleotide diversity
Age Speciation between P. falciparum and P. yoelii: 80 - 100 MYA, coincidencing with the speciation of the primate-rodent lineage (Perkins and Schall, 2002)

Speciation between P. falciparum and P. reichenowi: 5 - 7 MYA, coincidencing with the speciation of Homo-Pan lineage.
Speed 5.1 x 10-9 substitutions/site/year (Hughes and Verra, 2001).

The average rate of Syn substitution is about 5.75 - 7.19 substitution/Syn sites/109 Y based on the comparison of P. falciparum and P. yoelii (Castillo-Davis et al, 2004).

Meiotic crossover activity = 17 kb/cM, 5.88 x 10-7 recombination/site/generation (Su et al, 1999)

Effective
Populatoin
Size (Ne)

These "estimates are quite large and of a similar magnitude to those previously reported [Hughes and Verra F, 2001]. These estimates do not support the hypothesis of a severe recent population bottleneck." [Mu et al. Nature 418, 2002] mu is the neutral mutation rate (per gene or per base pair) per generation after [Hughes and Verra F, 2001].

The "effective population size of this species has been of the order of at least 10(5) for the past 300,000-400,000 years."  [Hughes AL, Verra F. . Proc. R. Soc. Lond. B 268, 1855–1860 (2001).]
Codon
Uasge 		from KAZUSA DNA Res. Inst, Japan

P. falciparum
P. vivax
P. yoelii yoelii
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