Chromosome Research

, Volume 20, Issue 2, pp 279–292

Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus

  • D. C. Cabral-de-Mello
  • G. T. Valente
  • R. T. Nakajima
  • C. Martins
Article

Abstract

To better understand genomic and chromosomal organization and evolutionary patterns of the U1 snRNA gene in cichlid fish, the gene was cytogenetically mapped and comparatively analyzed in 19 species belonging to several clades of the group. Moreover, the distribution and organization of U1 snRNA gene was analyzed in the Oreochromis niloticus genome. The results indicated high conservation of one chromosomal cluster of U1 snRNA in the African, Asian, and South American species, with few variations in the chromosomal position of the clusters in the South American species. The genomic analysis of U1 revealed a distinct scenario from that observed under the cytogenetic mapping. An enrichment of the U1 gene on linkage group (LG) 14 was observed that did not correspond to the same chromosome that harbors the U1 cluster identified by cytogenetic mapping. Moreover, it was revealed that the presence of several distinct transposable elements in the U1 gene flanking regions could be involved in the spreading of this sequence, but the generation of new, large snRNA clusters (detectable by fluorescent in situ hybridization, FISH) is apparently hampered. These results contribute to the understanding of multigene families' evolution and reinforce the utility of integrative analysis and the use of cytogenetic and bioinformatic methods to address the genomic and chromosomal evolutionary patterns of repeated DNAs among vertebrates. Moreover, the U1 gene represents a useful new chromosomal marker for cytogenetic studies.

Keywords

chromosomal evolution cytogenetic FISH genome multigene family Teleostei Cichlidae 

Abbreviation list

aa

Amino acid

BAC

Bacterial artificial chromosome

CLDN13

Claudin 13 gene

DAPI

4′,6-Diamidino-2-phenylindole

FISH

Fluorescence in situ hybridization

FR

Flanking region

FRU

Flanking region including the U1 gene

LG

Linkage group

MYA

Million years ago

NCBI

National Center for Biotechnology Information

NTS

Nontranscribed spacer

ORF

Open reading frame

PCR

Polymerase chain reaction

snRNA

Small nuclear RNA

TE

Transposable element

Supplementary material

10577_2011_9271_MOESM1_ESM.doc (106 kb)
Supplementary material S1a U1 snRNA gene copies identified in the O. niloticus genome version Tilapia_broad_v1 that were used as queries in the blast search against the NCBI nucleotide collection. The number of copies and their relative scaffolds are described. The numbers indicated by “|” represent the start and end positions in the scaffold. Bold, E value of blastn search. b The sequences of FRs used as queries in the blast search against the NCBI nucleotide collection. Up and down descriptions indicate that the sequences are upstream or downstream of the respective U1 copies. The numbers indicated by “|” represent the start and end positions in the scaffold. c The FRU sequences used as queries in Repbase analysis. The numbers indicated by “|” represent the start and end positions in the scaffold. Underlined bases represent the putative U1 copies; the arrow represents the direction of transcription. d The aa residues of translated ORFs with positive results after analysis in Repbase. These sequences were used as queries in Pfam analysis. The numbers indicated by “|” represents the start and end positions in the scaffold (DOC 106 kb)
10577_2011_9271_MOESM2_ESM.doc (41 kb)
Supplementary material S2Excluded regions of data presented in Fig. 1 (DOC 41 kb)
10577_2011_9271_MOESM3_ESM.doc (195 kb)
Supplementary material S3Blast results using the U1 copies of O. niloticus as queries against the NCBI nucleotide collection (DOC 195 kb)
10577_2011_9271_MOESM4_ESM.doc (70 kb)
Supplementary material S4Comparative analysis of blast results of U1_6 with other U1 results (DOC 70 kb)
10577_2011_9271_MOESM5_ESM.doc (26 kb)
Supplementary material S5Selection of representative blast results using the FRs of U1 snRNA gene as queries in the search against the NCBI nucleotide collection (DOC 26 kb)
10577_2011_9271_MOESM6_ESM.doc (1.2 mb)
Supplementary material S6Schematic representation of the overlap of the U1 copies (blue arrows) and U1_LV (Lytechinus variegatus; purple arrows). Box, details of the sequences of Lytechinus variegatus (purple arrows) and T. nigroviridis genomes (orange arrow). The sequence of new_U1 identified in Repbase and alignment with other U1 copies are also shown. The numbers indicated by “|” represent the start and end positions in the scaffold (DOC 1195 kb)
10577_2011_9271_MOESM7_ESM.doc (47 kb)
Supplementary material S7The aa residues of translated ORFs with positive results after analysis in Repbase followed by a table with a summary of the results obtained. The colors indicate the positions of the TEs in the sequences. The numbers indicated by “|” represent the start and end positions in the scaffold (DOC 47 kb)
10577_2011_9271_MOESM8_ESM.doc (368 kb)
Supplementary material S8Alignment of predicted aa residues of O. niloticus like-TEs and several TEs (L1-55_XT, L1-56_XT, KenoFr1, KenoDr1, Tx1-13). The yellow arrows indicate the Pfam identified domains (DOC 367 kb)

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • D. C. Cabral-de-Mello
    • 1
  • G. T. Valente
    • 2
  • R. T. Nakajima
    • 2
  • C. Martins
    • 2
  1. 1.Departamento de BiologiaUNESP—Univ Estadual Paulista, Instituto de Biociências/IBRio ClaroBrazil
  2. 2.Departamento de MorfologiaUNESP—Univ Estadual Paulista, Instituto de Biociências/IBBotucatuBrazil

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