Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

Additional file 1:

Distribution of the Bkm derived GACA/GATA repeats in the non-coding and coding genomes across the species. Chromosomes per haploid genome for respective species are also given in the table. Information on the presence of these repeats in genomes of Ovis aries and Capra hircus is not available due to their unfinished genomes.

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Additional file 2:

Occurrence of GACA repeats in the mRNA transcripts across the species. Some species such as Archeas, Arabidopsis thaliana, Zea mays, Dictyostelium discoideum, Ovis aries, Drosophila melanogaster and C. elegans lacked this repeat.

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Additional file 3:

Occurrence of GATA repeats in the mRNA transcripts across the species. Some species such as Archeas, Sus scrofa, Ovis aries, C. familiaris, C. elegans and D. discoideum were devoid of this repeat.

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Additional file 4:

List of primers used for identification of the transcripts, RT-PCR, Copy number calculation and Relative expressional studies. The primer IDs alongwith their respective gene accession numbers are also given in the table.

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Additional file 5:

Multiple sequence alignment of GACA-tagged 1.8 kb transcript from different somatic and gonadal tissues. Note the single nucleotide variations throughout the sequence. The variations shared by gonads and somatic tissues are highlighted in red, the ones common to somatic tissues in blue and gonad specific in pink. Note the exclusive major insertions of 36 and 5 bp in lung, highlighted in blue background, which were reconfirmed by sequencing this fragment from 5 different animals.

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Additional file 6:

Multiple nucleotide sequence alignment of GACA-tagged 1.3 kb transcript originating from different tissues and spermatozoa. The sequence from spermatozoa is highlighted in yellow background. The single nucleotide variations spread along the sequence shared by sperm and other tissues are highlighted in pink, and the ones common to tissues in blue. Several variations detected in sperm or testis only is shown in red. Note the exclusive insertion of 10 bp detected in sperm, highlighted in bold red and grey background.

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Additional file 7:

Multiple sequence alignment of GACA-tagged 850 bp transcript originating from different tissues and spermatozoa, homologous to HBGF-1. The sequence from the spermatozoa is highlighted in yellow background. The single nucleotide variations along the sequence but common across the tissues are highlighted in same color (pink or blue). Several variations detected in sperm or testis only are shown in red and the ones exclusive to ovary in blue background.

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Additional file 8:

Multiple sequence alignment of GACA-tagged 635 bp transcript originating from spermatozoa and different tissues, representing WASF2 gene. The sequence from spermatozoa is highlighted in yellow background. Several variations detected in sperm or testis only are shown in red, and that in somatic tissues are in blue color. Note the single nucleotide variations/insertions/deletions along the sequences from different tissues with highest frequency in testis.

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Additional file 9:

Multiple sequence alignment of GACA-tagged 523 bp transcript originating from testis, ovary and spermatozoa only, homologous to Ankyrin repeat domain-26. The sequence from spermatozoa is highlighted in yellow background. Note identical sequences in testis and spermatozoa (highlighted in red) in comparison to ovary (blue).

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Additional file 10:

Multiple sequence alignment of GATA-tagged 800 bp novel transcript originating from different tissues and spermatozoa. Note the single nucleotide variations/INDELS spread throughout the sequence. The variations common to tissues are highlighted in blue color and that shared by sperm in red. Note the exclusive and major insertions of 14 bp in spleen, highlighted in blue background.

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Additional file 11:

Multiple sequence alignment of GATA-tagged 425 bp novel transcript originating from different tissues and spermatozoa. The sequence from spermatozoa is highlighted in yellow background. The variations common to few tissues are highlighted in same color (blue or red).

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Additional file 12:

Cross-hybridization of genomic DNA from different species with the recombinant clones containing GACA (A) and GATA (B) uncovered genes/gene fragments. The names of the species are given on the top, and the autoradiograms for the respective gene/gene fragments on the left. Note the conservation of all the GATA and ~75% GACA uncovered genes across the species whereas remaining GACA-tagged transcripts were specific to buffalo/Bovids.

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