(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Eukaryota: NE > Opisthokonta: NE > Metazoa: NE > Eumetazoa: NE > Bilateria: NE > Deuterostomia: NE > Chordata: NE > Craniata: NE > Vertebrata: NE > Gnathostomata: NE > Teleostomi: NE > Euteleostomi: NE > Sarcopterygii: NE > Dipnotetrapodomorpha: NE > Tetrapoda: NE > Amniota: NE > Sauropsida: NE > Sauria: NE > Lepidosauria: NE > Squamata: NE > Bifurcata: NE > Gekkota: NE > Gekkonidae: NE > Gekkoninae: NE > Paroedura: NE > Paroedura picta: NE
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MMERSWMLWTFVEKWLLALASWSWGLCRISLLPLIVTFHLYGGMILPLLI FLSIAGILYKFQDVLLYFPEQPSSSRLYVPMPTGIPHENIFIRTKDGVLL NLILLRFTGDNPTFSPTVIYFHGNAGNIGHRLPNALLMLVNLKINLLLVD YRGYGKSEGEASEEGIYLDSEAVLDYVMTRSDLDKTKIFLFGRSLGGAVA IHLASENSHRISAIMVENTFLSIPHMASTLFSFFPMRYLPLWCYKNKFLS YRKIAQCRMPSLFISGLSDQLIPPVMMKQLYELSPARTKRLAIFPDGTHN DTWQCQGYFTALEQFIKEVSKSHSPEDMTKMSSNVTII
BACKGROUND: Conventionally, comparison among amniotes - birds, mammals, and reptiles - has often been approached through analyses of mammals and, for comparison, birds. However, birds are morphologically and physiologically derived and, moreover, some parts of their genomes are recognized as difficult to sequence and/or assemble and are thus missing in genome assemblies. Therefore, sequencing the genomes of reptiles would aid comparative studies on amniotes by providing more comprehensive coverage to help understand the molecular mechanisms underpinning evolutionary changes. RESULTS: Herein, we present the whole genome sequences of the Madagascar ground gecko (Paroedura picta), a promising study system especially in developmental biology, and used it to identify changes in gene repertoire across amniotes. The genome-wide analysis of the Madagascar ground gecko allowed us to reconstruct a comprehensive set of gene phylogenies comprising 13,043 ortholog groups from diverse amniotes. Our study revealed 469 genes retained by some reptiles but absent from available genome-wide sequence data of both mammals and birds. Importantly, these genes, herein collectively designated as 'elusive' genes, exhibited high nucleotide substitution rates and uneven intra-genomic distribution. Furthermore, the genomic regions flanking these elusive genes exhibited distinct characteristics that tended to be associated with increased gene density, repeat element density, and GC content. CONCLUSION: This highly continuous and nearly complete genome assembly of the Madagascar ground gecko will facilitate the use of this species as an experimental animal in diverse fields of biology. Gene repertoire comparisons across amniotes further demonstrated that the fate of a duplicated gene can be affected by the intrinsic properties of its genomic location, which can persist for hundreds of millions of years.
