Genome analysis - another nail for the Pogonophora coffin

Geoff Read g.read at niwa.cri.nz
Thu Mar 2 23:51:05 EST 2000


This new paper comments on several interesting matters (e.g., an annelid-
mollusk clade that excludes arthropods) , so it was difficult to decide what 
to put in the subject line ;-), but, anyway, watch for this one coming soon to 
a library near you.  

Boore, J.L., & W.M. Brown. 2000. Mitochondrial genomes of 
Galathealinum, Helobdella, and Platynereis: Sequence and gene 
arrangement comparisons indicate that Pogonophora is not a phylum and 
Annelida and Arthropoda are not sister taxa. -- Molecular Biology and 
Evolution, 17(1):87-106.  

ABSTRACT. We report a contiguous region of more than half (>7,500 nt) 
of the mitochondrial genomes for Platynereis dumerii (Annelida: 
Polychaeta), Helobdella robusta (Annelida: Hirudinida), and Galathealinum 
brachiosum (Pogonophora: Perviata). The relative arrangements of all 22 
genes identified for Helobdella and Galathealinum are identical to one 
another and to their arrangements in the mtDNA of the previously studied 
oligochaete annelid Lumbricus. In contrast, Platynereis differs from these 
taxa in the positions of several tRNA genes and in having two additional 
tRNA genes (trnC and trnM) and a large noncoding sequence in this 
region. Comparisons of relative gene arrangements and of the nucleotide 
and inferred amino acid sequences among these and other published taxa 
provide strong support for an annelid- mollusk clade that excludes 
arthropods, and for the inclusion of pogonophorans within Annelida, rather 
than giving them separate phylum status. Gene arrangement comparisons 
include the first use of a recently described method on previously 
unpublished data. Although a variety of alternative initiation codons are 
typically used by mitochondrial protein-encoding genes, ATG appears to 
be the initiator for all but one reported here. The large noncoding region 
(1,091 nt) identified in Platynereis has no significant sequence similarity to 
the noncoding region of Lumbricus, although each contains runs of TA 
dinucleotides and of homopolymers, which could potentially serve as 
signaling elements. There is strong bias for synonymous codon usage in 
Helobdella and especially in Galathealinum. In this latter taxon, 5 codons 
are completely unused, 13 are used three or fewer times, and G appears at 
third codon positions in only 26 of the 2,236 codons. Nucleotide 
composition bias appears to influence amino acid composition of the 
proteins.  


--
  Geoff Read <g.read at niwa.cri.nz>


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