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Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus

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Abstract

The order Rodentia and in particular the Muridae are characterised by extremely high rates of chromosome evolution and remarkable chromosome diversity. The Praomys group (Murinae, Muridae and Rodentia) constitutes a diverse and abundant group divided into two complexes, the jacksoni complex and the tullbergi complex which includes the species Praomys tullbergi. Comparative chromosome painting using the two index genomes, Mus musculus and Rattus norvegicus, was performed resulting in a high resolution chromosome map for P. tullbergi. The combined use of rat and mouse probes and the assistance of the assembly of all the available sequencing data from Ensembl genome browser allowed a great dissection of P. tullbergi genome, the detection of inversion events and ultimately the refinement of P. tullbergi comparative map. A key achievement was the reconstruction of a high precision Muroidea ancestral karyotype (Muridae/Cricetidae and Murine) based in a broad species analysis combining previous reported comparative maps together with the presented data. This permitted the reconstruction of the evolutionary history of chromosome changes since the ancestral Muroidea genome and enlightened the phylogenetic relationships with the related species mouse and rat. The analysis of constitutive heterochromatin and its co-localisation with the identified evolutionary breakpoints regions was performed suggesting the involvement of repetitive sequences in the chromosome rearrangements that originated the present P. tullbergi genome architecture.

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Abbreviations

AMK:

Ancestral Muroidea karyotype

CH:

Constitutive heterochromatin

DOP-PCR:

Degenerated oligonucleotide primed-PCR

FACS:

Fluorescence-activated cell sorter

FITC:

Fluorescein isothiocyanate

GTG:

G-banding by trypsin using Giemsa

HSA:

Homo sapiens

MMU:

Mus musculus

PTU:

Praomys tullbergi

RNO:

Rattus norvegicus

TAMRA:

Tetramethyl-6-carboxyrhodamine

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Acknowledgments

This work was supported by the project POCI/BIA-BCM/58541/2004, a research position on Animal Genomics of the ‘Sistema Científico e Tecnológico Nacional-Ciência 2007’ and the PhD grants SFRH/BD/25813/2005 and SFRH/BD/41576/2007, all from the Science and Technology Foundation (FCT) from Portugal. We are deeply grateful to Dr. Vitaly Volobouev for providing the cell cultures of P. tullbergi.

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Correspondence to Raquel Chaves.

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Responsible Editor: Herbert Macgregor.

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S1

Schematic presentation of the integrative in silico analysis (Ensembl sequencing data from the Synteny tool with our data) that led to the inference of the rat (RNO) and mouse (MMU) chromosome homologies to human (HSA). The example for chromosome PTU5 is shown. S1a. The use of both index species (rat and mouse) paint probes onto Praomys tullbergi (PTU) chromosomes allowed the specific delineation of homologies between RNO and MMU. In this specific case RNO4 to MMU5 and MMU6. With the assistance of Ensembl Synteny assemblies it was then possible to unequivocally determine the exact homology chromosome segment between each synteny block of Mus musculus and Rattus norvegicus. This data integration also allowed to designate as proximal, median and distal the different syntenic blocks regarding its position in relation to the centromere. In the example shown, RNO4prox is homologous to MMU5prox and RNO4dist to the entire RNO6. S1b. The accuracy of this analysis allowed to further assign the homologies between each rodent index species and human. And from this standpoint to P. tullbergi chromosomes. RNO4prox/MMU5prox showed to be homologous to HSA7. RNO4dist/MMU6 showed to be homologous to HSA7, HSA4, HSA2, HSA3, HSA10 and HSA12. Highlighted is HSA7, whose homologies to MMU and RNO shown to confirm the results above. This is evident when comparing segments marked with black squares or circles in both Ensembl synteny maps (HSA7 to RNO and MMU): black squares correspond to RNO4dist/MMU6 and circles correspond to RNO4prox/MMU5prox (PDF 2,033 kb)

S2

Test of consistency of rat and mouse painting in P. tullbergi chromosomes showing the common derived syntenic associations in PTU/MMU vs. RNO and PTU/RNO vs. MMU (PDF 5 kb)

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Chaves, R., Louzada, S., Meles, S. et al. Praomys tullbergi (Muridae, Rodentia) genome architecture decoded by comparative chromosome painting with Mus and Rattus . Chromosome Res 20, 673–683 (2012). https://doi.org/10.1007/s10577-012-9304-1

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