Comparison of the Complete ATP-Binding Cassette(ABC) transporters of C. elegans and C. Briggsae: Orthology and Divergence Export

@article{citeulike:3297493, abstract = {ABC transporters constitute one of the biggest gene families in C. elegans. They are mostly involved in transmembrane delivery of substrates such as amino acids, peptides and toxins. In order to understand how big gene families are organized and how they evolve, comparative analysis of the ABC transporters has been done on a genome scale between C.elegans and C. briggsae now that both of genome sequences are available. 59 ABC genes have been identified and classified into 8 different subfamilies in C.elegans by a combination of database search and phylogenetic analysis. Two genes, C56E6.5 and C56E6.1, in C.elegans , cannot be assigned into established human subfamilies and has been assigned to a new subfamily H. Each subfamily shows similar structure to the equivalent human one. Annotation of C. briggsae ABC transporters has been done by database search, ab initio gene prediction, and the use of syntenic relationships. It turns out that ABC transporters are well conserved between the two morphologically similar worms. 57 putative orthologous ABC transporters in C.briggsaehave been identified which can also be grouped into 8 subfamilies, and only 3 of C. elegans ABC genes do not have an obvious ortholog in C. Briggsae. Most of the C. briggsae ABC transporters are of comparable size to their orthologs in C. elegans. 6 inversions and 5 deletions/insertions were found among the nearest neighbours of the 57 orthologous pairs. 45 of the 57 C. Briggsae orthologous ABC genes were confirmed both by syntenic and phylogenetic analysis. 6 putative C. briggsae ABC orthologs assigned by BLAST score don't have any syntenic support, but 4 of them are clustered well with their C.elegans orthologues when ABC transporters from both species are used to generate a phylogenetic tree. 14 C. Briggsae ABC genes are not supported by the tree data, suggesting possible mis-prediction or sequence error. The transposase or reverse transcriptase insertion were found within two gene clusters in C. briggsae, suggesting the role of transposition in the formation of local gene clusters. Two C. briggsae ABC genes are assigned only by sequence similarity and have no tree or syntenic support, suggesting transposition or misprediction. No significant ortholog can be found for one of the C. elegans ABC transporters, Y57G11C.1. However, as there is no EST match for this gene in the database, it is possible that the gene is a pseudogene, which has therefore undergone a great deal of mutation. Also, local duplication occurs more frequently for ABCs on the sex chromosome than on autosomes. We are investigating the expression pattern of all the ABC transporters in C.elegans using GFP as markers, those having the same tissue expression will be used to map transcriptional elements. The orthology information will facilitate the identification of some cis-elements shared between the two species.}, author = {Zhao, Zhongying and Sheps, Jonathan and Ling, Victor and Tyson, John and Baillie, David L.}, citeulike-article-id = {3297493}, citeulike-linkout-0 = {http://www.wormbase.org/db/misc/paper?name=WBPaper00015815}, journal = {Worm Breeder's Gazette}, keywords = {abch-1, abcx-1, c56e61, c56e65, c\_elegans, caenorhabditis\_elegans, celegans, elegans, gazette\_abstract, nematode, wormbase}, posted-at = {2008-09-20 10:13:42}, priority = {3}, title = {Comparison of the Complete ATP-Binding Cassette(ABC) transporters of C. elegans and C. Briggsae: Orthology and Divergence}, url = {http://www.wormbase.org/db/misc/paper?name=WBPaper00015815}, volume = {17}, year = {2002} }

TY - JOUR ID - citeulike:3297493 L3 - citeulike-article-id:3297493 N2 - ABC transporters constitute one of the biggest gene families in C. elegans. They are mostly involved in transmembrane delivery of substrates such as amino acids, peptides and toxins. In order to understand how big gene families are organized and how they evolve, comparative analysis of the ABC transporters has been done on a genome scale between C.elegans and C. briggsae now that both of genome sequences are available. 59 ABC genes have been identified and classified into 8 different subfamilies in C.elegans by a combination of database search and phylogenetic analysis. Two genes, C56E6.5 and C56E6.1, in C.elegans , cannot be assigned into established human subfamilies and has been assigned to a new subfamily H. Each subfamily shows similar structure to the equivalent human one. Annotation of C. briggsae ABC transporters has been done by database search, ab initio gene prediction, and the use of syntenic relationships. It turns out that ABC transporters are well conserved between the two morphologically similar worms. 57 putative orthologous ABC transporters in C.briggsaehave been identified which can also be grouped into 8 subfamilies, and only 3 of C. elegans ABC genes do not have an obvious ortholog in C. Briggsae. Most of the C. briggsae ABC transporters are of comparable size to their orthologs in C. elegans. 6 inversions and 5 deletions/insertions were found among the nearest neighbours of the 57 orthologous pairs. 45 of the 57 C. Briggsae orthologous ABC genes were confirmed both by syntenic and phylogenetic analysis. 6 putative C. briggsae ABC orthologs assigned by BLAST score don't have any syntenic support, but 4 of them are clustered well with their C.elegans orthologues when ABC transporters from both species are used to generate a phylogenetic tree. 14 C. Briggsae ABC genes are not supported by the tree data, suggesting possible mis-prediction or sequence error. The transposase or reverse transcriptase insertion were found within two gene clusters in C. briggsae, suggesting the role of transposition in the formation of local gene clusters. Two C. briggsae ABC genes are assigned only by sequence similarity and have no tree or syntenic support, suggesting transposition or misprediction. No significant ortholog can be found for one of the C. elegans ABC transporters, Y57G11C.1. However, as there is no EST match for this gene in the database, it is possible that the gene is a pseudogene, which has therefore undergone a great deal of mutation. Also, local duplication occurs more frequently for ABCs on the sex chromosome than on autosomes. We are investigating the expression pattern of all the ABC transporters in C.elegans using GFP as markers, those having the same tissue expression will be used to map transcriptional elements. The orthology information will facilitate the identification of some cis-elements shared between the two species. JF - Worm Breeder's Gazette TI - Comparison of the Complete ATP-Binding Cassette(ABC) transporters of C. elegans and C. Briggsae: Orthology and Divergence VL - 17 KW - abch-1 KW - abcx-1 KW - c56e61 KW - c56e65 KW - c_elegans KW - caenorhabditis_elegans KW - celegans KW - elegans KW - gazette_abstract KW - nematode KW - wormbase AU - Zhao, Zhongying AU - Sheps, Jonathan AU - Ling, Victor AU - Tyson, John AU - Baillie, David PY - 2002/// UR - http://www.wormbase.org/db/misc/paper?name=WBPaper00015815 ER -