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  The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly

Roscito, J. G., Sameith, K., Pippel, M., Kees-Jan, F., Winkler, S., Dahl, A., et al. (2018). The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly. GigaScience, 7(12): giy141. doi:10.1093/gigascience/giy141.

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The genome of the tegu lizard Salvator merianae
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 Creators:
Roscito, Juliana G.1, Author           
Sameith, Katrin1, Author           
Pippel, Martin2, Author
Kees-Jan, Francoijs2, Author
Winkler, Sylke2, Author
Dahl, Andreas2, Author
Papoutsoglou, Georg2, Author
Myers, Gene2, Author
Hiller, Michael1, Author           
Affiliations:
1Max Planck Institute for the Physics of Complex Systems, Max Planck Society, ou_2117288              
2External Organizations, ou_persistent22              

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 MPIPKS: Living matter
 Abstract: Background
Reptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes.
Results
Here, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences long-read, and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (<20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades.
Conclusions
The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.

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 Dates: 2018-11-272018-12-01
 Publication Status: Issued
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 Identifiers: DOI: 10.1093/gigascience/giy141
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Title: GigaScience
Source Genre: Journal
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Publ. Info: London : BioMed Central
Pages: - Volume / Issue: 7 (12) Sequence Number: giy141 Start / End Page: - Identifier: ISSN: 2047-217X
CoNE: https://pure.mpg.de/cone/journals/resource/2047-217X