Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes.
Sequencing and comparative analyses of genomes from multiple vertebrates are providing insights about the genetic basis for biological diversity. To date, these efforts largely have focused on eutherian mammals, chicken, and fish. In this article, we describe the generation and study of genomic sequences from noneutherian mammals, a group of species occupying unusual phylogenetic positions. A large sequence data set (totaling >5 Mb) was generated for the same orthologous region in three marsupial (North American opossum, South American opossum, and Australian tammar wallaby) and one monotreme (platypus) genomes. These ancient mammalian genomes are characterized by unusual architectural features with respect to G + C and repeat content, as well as compression relative to human. Approximately 14% and 34% of the human sequence forms alignments with the orthologous sequence from platypus and the marsupials, respectively; these numbers are distinctly lower than that observed with nonprimate eutherian mammals (45-70%). The alignable sequences between human and each marsupial species are not completely overlapping (only 80% common to all three species) nor are the platypus-alignable sequences completely contained within the marsupial-alignable sequences. Phylogenetic analysis of synonymous coding positions reveals that platypus has a notably long branch length, with the human-platypus substitution rate being on average 55% greater than that seen with human-marsupial pairs. Finally, analyses of the major mammalian lineages reveal distinct patterns with respect to the common presence of evolutionarily conserved vertebrate sequences. Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome.
Margulies
Elliott H
EH
Genome Technology Branch and NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Maduro
Valerie V B
VV
Thomas
Pamela J
PJ
Tomkins
Jeffery P
JP
Amemiya
Chris T
CT
Luo
Meizhong
M
Green
Eric D
ED
D000818:Animals; D005075:Biological Evolution; D016678:Genome; D006801:Humans; D008394:Marsupialia / Q000235:genetics*; D008969:Molecular Sequence Data; D009007:Monotremata / Q000235:genetics*; D010802:Phylogeny
J Mol Biol. 2000 May 5;298(3):365-77
10772856
J Mol Evol. 2002 Jan;54(1):71-80
11734900
Genome Res. 2004 Apr;14(4):708-15
15060014
Mol Biol Evol. 2004 Mar;21(3):468-88
14660683
Nat Rev Genet. 2003 Apr;4(4):251-62
12671656
Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):13994-4001
15292512
Science. 2002 Aug 23;297(5585):1301-10
12142439
Science. 2001 Dec 14;294(5550):2348-51
11743200
Genome Res. 2002 Aug;12(8):1269-76
12176934
Trends Genet. 2002 Oct;18(10):517-21
12350341
Mamm Genome. 2001 Jul;12(7):513-7
11420613
Comp Biochem Physiol A Mol Integr Physiol. 2003 Dec;136(4):867-81
14667850
Nat Genet. 2003 Apr;33(4):514-7
12612582
Trends Genet. 2002 Feb;18(2):104-8
11818143
Mol Phylogenet Evol. 2003 Aug;28(2):360-85
12878472
Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):803-8
11792858
Mol Phylogenet Evol. 2003 Aug;28(2):171-85
12878457
Nature. 2003 Aug 14;424(6950):788-93
12917688
Genome Res. 2004 Apr;14(4):539-48
15059994
EMBO Rep. 2003 Feb;4(2):143-7
12612602
Curr Opin Genet Dev. 2003 Dec;13(6):604-10
14638322
Nature. 2004 Dec 9;432(7018):695-716
15592404
Genome Res. 2003 Jan;13(1):64-72
12529307
Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2869-74
10077603
Cold Spring Harb Symp Quant Biol. 2003;68:255-63
15338625
Genomics. 2003 Mar;81(3):249-59
12659809
Genome Res. 2000 Jul;10(7):939-49
10899143
Nature. 2001 Feb 15;409(6822):860-921
11237011
Genome Res. 2003 Dec;13(12):2507-18
14656959
Nature. 1967 Jul 8;215(5097):192-3
6049118
Genome Res. 2004 Apr;14(4):700-7
15060013
Nature. 1998 Apr 30;392(6679):917-20
9582070
Mol Phylogenet Evol. 1998 Jun;9(3):585-98
9668008
J Physiol. 2004 Jan 1;554(Pt 1):31-9
14678488
Nature. 2002 Dec 5;420(6915):520-62
12466850