TY - JOUR
T1 - Human and nematode orthologs - Lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans
AU - Wheelan, Sarah J.
AU - Boguski, Mark S.
AU - Duret, Laurent
AU - Makalowski, Wojciech
PY - 1999/9/30
Y1 - 1999/9/30
N2 - Recently, we have defined and analyzed over 1800 orthologous human and rodent genes. Here we extend this work to compare human and Caenorhabditis elegans coding sequences. 1880 human proteins were compared with about 20,000 predicted nematode proteins presumably comprising nearly the complete proteome of C. elegans. We found that 44% of human/rodent orthologs have convincing nematode counterparts. On average, the amino acid similarity and identity between aligned human and C. elegans orthologous gene products are 69.3% and 49.1% respectively, and the nucleotide identity is 49.8%. Detailed investigation of our results suggests that some nematode gene predictions are incorrect, leading to erroneous pairing with human genes (e.g. calcineurin and polymerase II elongation factor III). Furthermore, other proteins (i.e. homologs of human ribosomal proteins S20 and L41, thymosin) are missing entirely from the nematode proteome, suggesting that it may not be complete. These results underscore the fact that metazoan gene prediction is a very challenging task and that most computer-predicted nematode genes require supporting evidence of their existence from comparative genomics and/or laboratory investigation. (C) 1999 Elsevier Science B.V. All rights reserved.
AB - Recently, we have defined and analyzed over 1800 orthologous human and rodent genes. Here we extend this work to compare human and Caenorhabditis elegans coding sequences. 1880 human proteins were compared with about 20,000 predicted nematode proteins presumably comprising nearly the complete proteome of C. elegans. We found that 44% of human/rodent orthologs have convincing nematode counterparts. On average, the amino acid similarity and identity between aligned human and C. elegans orthologous gene products are 69.3% and 49.1% respectively, and the nucleotide identity is 49.8%. Detailed investigation of our results suggests that some nematode gene predictions are incorrect, leading to erroneous pairing with human genes (e.g. calcineurin and polymerase II elongation factor III). Furthermore, other proteins (i.e. homologs of human ribosomal proteins S20 and L41, thymosin) are missing entirely from the nematode proteome, suggesting that it may not be complete. These results underscore the fact that metazoan gene prediction is a very challenging task and that most computer-predicted nematode genes require supporting evidence of their existence from comparative genomics and/or laboratory investigation. (C) 1999 Elsevier Science B.V. All rights reserved.
KW - Comparative genomics
KW - Molecular evolution
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U2 - 10.1016/S0378-1119(99)00298-X
DO - 10.1016/S0378-1119(99)00298-X
M3 - Article
C2 - 10570994
AN - SCOPUS:0032835248
SN - 0378-1119
VL - 238
SP - 163
EP - 170
JO - Gene
JF - Gene
IS - 1
ER -