Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

Abstract

BackgroundWith the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs) from the American alligator (Alligator mississippiensis), painted turtle (Chrysemys picta) and emu (Dromaius novaehollandiae) to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken.ResultsFrom a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%), 24 (turtle, 1.3%) and 479 (emu, 16.3%) pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes.ConclusionOur results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the genomes of reptilian and avian ancestors led to the ~50% reduction in genome size observed in birds compared to reptiles. We have also mapped and identified likely gene regions in hundreds of new BAC clones from these species.

Gonadal Differentiation in Reptiles Exhibiting Environmental Sex Determination

“…Fragments of chromosomes associated with one sex, identified by chromosome painting, have also proved successful at revealing loci associated with GSD [Valleley et al, 1994]. More recently, restriction site-associated DNA sequencing has been applied to discover allelic differences showing a strong association to a specific sex [Chapus and Edwards, 2009]. In addition, potential effects of incubation temperature on sex determination and the pattern of TSD can be identified by the maximum likelihood model selection [Godfrey et al, 2003].…”

Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

“…Wicker et al [2005] used a different approach to analyze the Cot library of chicken and provided an extensive analysis of the chicken TE complement. By using partial genome data (end sequences of BAC clones) of tuatara, another species of Anolis , 2 turtles, 2 crocodiles and emu, a first insight into the organization of TE repertoires in all major sauropsid lineages was gained [Shedlock, 2006;Shedlock et al, 2007;Chapus and Edwards, 2009;Shan et al, 2009]. Availability of the first draft of the Anolis genome enabled the first studies of TE complement in lizards at the genome level [Novick et al, 2009;Piskurek et al, 2009].…”

“…In sauropsids, the most intensively investigated TEs have been non-LTR retrotransposons (LINEs or retroposons), such as RTE clade (including Bov-B LINEs) [Zupunski et al, 2001;Gogolevsky et al, 2008;Novick et al, 2009;Piskurek et al, 2009], L2 clade [Lovsin et al, 2001;Novick et al, 2009;Piskurek et al, 2009], L1 clade [Kordis et al, 2006;Novick et al, 2009;Piskurek et al, 2009], R4 clade [Volff et al, 2001a;Novick et al, 2009;Piskurek et al, 2009], CR1 clade [Fantaccione et al, 2004;International Chicken Genome Sequencing Consortium, 2004;Wicker et al, 2005;Shedlock, 2006;Kaiser et al, 2007;Kriegs et al, 2007;Shedlock et al, 2007;Abrusan et al, 2008;Chapus and Edwards, 2009;Liu et al, 2009;Novick et al, 2009;Piskurek et al, 2009;Shan et al, 2009] and R2 clade [Kojima and Fujiwara, 2005]. Much research in sauropsids has been focused on SINEs, such as on the CR1 LINE/SINE pair in a lizard [Fantaccione et al, 2004], LF SINEs [Bejerano et al, 2006], AmnSINE1s [Nishihara et al, 2006;Hirakawa et al, 2009], Sauria SINEs [Piskurek et al, 2006[Piskurek et al, , 2009Piskurek and Okada, 2007;Gogolevsky et al, 2008;Kosushkin et al, 2008], polIII/SINE in turtles …”

“…Therefore an initiative started with the preparation of BAC libraries of the key reptilian and bird lineages (tuatara, lizard, turtle, alligator and emu) [Shedlock, 2006;Wang et al, 2006;Shedlock et al, 2007;Chapus and Edwards, 2009;Shan et al, 2009]. The first attempt to reveal the structure of the ancestral amniote genome was made by analyzing the end sequences of BAC clones from the above mentioned sauropsid species [Shedlock, 2006;Shedlock et al, 2007].…”

“…The analyses of draft genomes of chicken [International Chicken Genome Sequencing Consortium, 2004;Wicker et al, 2005;Abrusan et al, 2008], Anolis [Novick et al, 2009;Piskurek et al, 2009] and other preliminary reptilian genome sequencing projects [Wang et al, 2006;Organ et al, 2007;Shedlock et al, 2007;Chapus and Edwards, 2009;Shan et al, 2009] have provided invaluable information concerning the diversity, activity and TE landscapes in sauropsids. The large amount of recently accumulated data on TEs in diverse lineages of sauropsids has provided a timely opportunity to review the current knowledge about transposable elements of sauropsids in their genomic context.…”