A Genetic Linkage Map for Zebrafish: Comparative Analysis and Localization of Genes and Expressed Sequences

Genetic screens in zebrafish (Danio rerio) have isolated mutations in hundreds of genes with essential functions. To facilitate the identification of candidate genes for these mutations, we have genetically mapped 104 genes and expressed sequence tags by scoring single-strand conformational polymorphisms in a panel of haploid siblings. To integrate this map with existing genetic maps, we also scored 275 previously mapped genes, microsatellites, and sequence-tagged sites in the same haploid panel. Systematic phylogenetic analysis defined likely mammalian orthologs of mapped zebrafish genes, and comparison of map positions in zebrafish and mammals identified significant conservation of synteny. This comparative analysis also identified pairs of zebrafish genes that appear to be orthologous to single mammalian genes, suggesting that these genes arose in a genome duplication that occurred in the teleost lineage after the divergence of fish and mammal ancestors. This comparative map analysis will be useful in predicting the locations of zebrafish genes from mammalian gene maps and in understanding the evolution of the vertebrate genome.

Download Full-text

VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽

10.1093/aobpla/plaa064 ◽

2020 ◽

Vol 12 (6) ◽

Author(s):

Morad M Mokhtar ◽

Ebtissam H A Hussein ◽

Salah El-Din S El-Assal ◽

Mohamed A M Atia

Keyword(s):

Vicia Faba ◽

Faba Bean ◽

Expressed Sequence Tags ◽

Genetic Linkage ◽

Genetic Maps ◽

Linkage Maps ◽

Microrna Target ◽

Genetic Linkage Maps ◽

Expressed Sequence ◽

Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Download Full-text

Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos

Aquaculture ◽

10.1016/j.aquaculture.2004.10.012 ◽

2005 ◽

Vol 243 (1-4) ◽

pp. 69-81 ◽

Cited By ~ 25

Author(s):

Elena Sarropoulou ◽

Deborah Mary Power ◽

Antonios Magoulas ◽

Robert Geisler ◽

Georgios Kotoulas

Keyword(s):

Comparative Analysis ◽

Expressed Sequence Tags ◽

Sparus Aurata ◽

Gilthead Sea Bream ◽

Sea Bream ◽

Expressed Sequence

Download Full-text

Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library

Mammalian Genome ◽

10.1007/s003359900816 ◽

1998 ◽

Vol 9 (7) ◽

pp. 545-549 ◽

Cited By ~ 34

Author(s):

R.Z. Ma ◽

M.J.T. van Eijk ◽

J.E. Beever ◽

G. Guérin ◽

C.L. Mummery ◽

...

Keyword(s):

Comparative Analysis ◽

Cdna Library ◽

Expressed Sequence Tags ◽

Expressed Sequence

Download Full-text

Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences

Canadian Journal of Microbiology ◽

10.1139/w10-103 ◽

2011 ◽

Vol 57 (2) ◽

pp. 84-90 ◽

Cited By ~ 17

Author(s):

Danyu Shen ◽

Wenwu Ye ◽

Suomeng Dong ◽

Yuanchao Wang ◽

Daolong Dou

Keyword(s):

Comparative Analysis ◽

Alternative Splicing ◽

Expressed Sequence Tags ◽

Phytophthora Sojae ◽

Genomic Sequences ◽

Splice Sites ◽

Distinct Phylogenetic Lineage ◽

Expressed Sequence ◽

Complete Genomic

The oomycetes, a distinct phylogenetic lineage of fungus-like microorganisms, are heterokonts (stramenopiles) belonging to the supergroup Chromalveolata. Although the complete genomic sequences of a number of oomycetes have been reported, little information regarding the introns therein is available. Here, we investigated the introns of Phytophthora sojae , a pathogen that causes soybean root and stem rot, by a comparative analysis of genomic sequences and expressed sequence tags. A total of 4013 introns were identified, of which 96.6% contained canonical splice sites. The P. sojae genome possessed features distinct from other organisms at 5′ splice sites, polypyrimidine tracts, branch sites, and 3′ splice sites. Diverse repeating sequences, ranging from 2 to 10 nucleotides in length, were found at more than half of the intron–exon boundaries. Furthermore, 122 genes underwent alternative splicing. These data indicate that P. sojae has unique splicing mechanisms, and recognition of those mechanisms may lead to more accurate predictions of the location of introns in P. sojae and even other oomycete species.

Download Full-text