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Third party data gene data set of eutherian growth hormone genes.

Premzl M - Genom Data (2015)

Bottom Line: The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes.The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments.The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genomics, Centre of Animal Reproduction, 55 Heinzel St, Zagreb, Croatia.

ABSTRACT
Among 146 potential coding sequences, the most comprehensive eutherian growth hormone gene data set annotated 100 complete coding sequences. The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes. The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments. The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.

No MeSH data available.


(A) Phylogenetic analysis of eutherian growth hormone genes. The minimum evolution tree was calculated using maximum composite likelihood method. After 1000 bootstrap replicates, the estimates higher than 50% were shown. (B) Distribution of common cysteine amino acid residues in eutherian growth hormone proteins. The common Cys amino acid residues 1–6 were labelled using black rectangles. The numbers indicated numbers of amino acid residues. (C) Reference human GHA1 protein primary structure. The 4 invariant amino acid sites were shown using white letters on black backgrounds and 13 forward amino acid sites were shown using white letters on grey backgrounds. The common Cys amino acid residues 1–6 were labelled below reference protein amino acid sequence, as well as 14 predicted functional amino acid residues (#) [9]. The α-helical regions of human GHA1 tertiary structure 1N9D were labelled by rectangles [9]. The tertiary structure determinant amino acid sites H75 and H88 were indicated by arrows [10]. The predicted signal peptide cleavage site was indicated by black triangle.
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f0005: (A) Phylogenetic analysis of eutherian growth hormone genes. The minimum evolution tree was calculated using maximum composite likelihood method. After 1000 bootstrap replicates, the estimates higher than 50% were shown. (B) Distribution of common cysteine amino acid residues in eutherian growth hormone proteins. The common Cys amino acid residues 1–6 were labelled using black rectangles. The numbers indicated numbers of amino acid residues. (C) Reference human GHA1 protein primary structure. The 4 invariant amino acid sites were shown using white letters on black backgrounds and 13 forward amino acid sites were shown using white letters on grey backgrounds. The common Cys amino acid residues 1–6 were labelled below reference protein amino acid sequence, as well as 14 predicted functional amino acid residues (#) [9]. The α-helical regions of human GHA1 tertiary structure 1N9D were labelled by rectangles [9]. The tertiary structure determinant amino acid sites H75 and H88 were indicated by arrows [10]. The predicted signal peptide cleavage site was indicated by black triangle.

Mentions: The BioEdit 7.0.5.3 program was used in nucleotide and protein sequence analyses (http://www.mbio.ncsu.edu/BioEdit/bioedit.html). The NCBI's BLAST programs were used in identification of genes in eutherian genomic sequence assemblies downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/ and ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/) [2], [3]. Alternatively, the Ensembl genome browser's BLAST or BLAT web tools were used in gene identifications (http://www.ensembl.org). The gene feature analyses included direct evidence of eutherian gene annotations deposited in NCBI's nr, est_human, est_mouse and est_others databases (http://www.ncbi.nlm.nih.gov). The protocol tested potential growth hormone (GH) coding sequences using tests of reliability of eutherian public genomic sequences. Using NCBI's BLAST programs and primary sequence reads deposited in NCBI's Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi), the first test step analysed nucleotide sequence coverage of potential coding sequences. The potential coding sequences were described as complete coding sequences in second test step only if consensus trace sequence coverage was available for every nucleotide. Alternatively, the potential coding sequences were described as putative coding sequences. Only the complete GH coding sequences were deposited in European Nucleotide Archive (http://www.ebi.ac.uk/ena/about/tpa-policy) and used in phylogenetic and protein molecular evolution analyses. In gene descriptions, the guidelines of human and mouse gene nomenclature were followed (http://www.genenames.org/about/guidelines and http://www.informatics.jax.org/mgihome/nomen/gene.shtml). There were 100 complete eutherian GH coding sequences, among 146 potential coding sequences (Fig. 1) (Supplementary data file 1). The most comprehensive third party data gene data set of eutherian GH genes annotated 15 GHA genes, 36 GHB genes, 5 GHC genes, 39 GHD genes and 5 GHE genes. The eutherian GHA genes were described as prolactin PRL orthologues, eutherian GHB genes were described as growth hormone GH orthologues and paralogues, domesticated guinea pig GHC genes were first described in present work, Ghd genes were described as prolactin paralogues in mouse and brown rat and GHE genes were described as prolactin paralogues in domestic cattle [4], [5], [6]. The masking of transposable elements using RepeatMasker version open-4.0.3 was included as preparatory step in multiple pairwise genomic sequence alignments, using default settings except simple repeats and low complexity elements were not masked (sensitive mode, cross_match version 1.080812, RepBase Update 20130422, RM database version 20130422) (http://www.repeatmasker.org/). In genomic sequence alignments, the mVISTA web tool was used, using AVID alignment program and default settings (http://genome.lbl.gov/vista/index.shtml). Using ClustalW implemented in BioEdit 7.0.5.3, the common predicted promoter genomic sequence regions were aligned at nucleotide sequence level and then manually corrected. The pairwise nucleotide sequence identities of common predicted promoter genomic sequence regions were calculated using BioEdit 7.0.5.3, and used in statistical analysis (Microsoft Office Excel). The common predicted promoter genomic sequence regions of eutherian GHA and GHB genes were described (Supplementary data file 2, Supplementary data file 3). For example, among primates, the calculated patterns of average pairwise nucleotide sequence identities of common predicted promoter genomic sequence regions exceeded empirically determined cut-offs of detection of common genomic sequence regions. Whereas the average pairwise nucleotide sequence identity of primate GHA common predicted promoter genomic sequence regions was ā = 0,872 (amax = 0,986, amin = 0,767, āad = 0,074) (Supplementary data file 2, Supplementary data file 3), average pairwise nucleotide sequence identity of primate GHB common predicted promoter genomic sequence regions was ā = 0,844 (amax = 0,989, amin = 0,252, āad = 0,111) (Supplementary data file 2, Supplementary data file 3).


Third party data gene data set of eutherian growth hormone genes.

Premzl M - Genom Data (2015)

(A) Phylogenetic analysis of eutherian growth hormone genes. The minimum evolution tree was calculated using maximum composite likelihood method. After 1000 bootstrap replicates, the estimates higher than 50% were shown. (B) Distribution of common cysteine amino acid residues in eutherian growth hormone proteins. The common Cys amino acid residues 1–6 were labelled using black rectangles. The numbers indicated numbers of amino acid residues. (C) Reference human GHA1 protein primary structure. The 4 invariant amino acid sites were shown using white letters on black backgrounds and 13 forward amino acid sites were shown using white letters on grey backgrounds. The common Cys amino acid residues 1–6 were labelled below reference protein amino acid sequence, as well as 14 predicted functional amino acid residues (#) [9]. The α-helical regions of human GHA1 tertiary structure 1N9D were labelled by rectangles [9]. The tertiary structure determinant amino acid sites H75 and H88 were indicated by arrows [10]. The predicted signal peptide cleavage site was indicated by black triangle.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664738&req=5

f0005: (A) Phylogenetic analysis of eutherian growth hormone genes. The minimum evolution tree was calculated using maximum composite likelihood method. After 1000 bootstrap replicates, the estimates higher than 50% were shown. (B) Distribution of common cysteine amino acid residues in eutherian growth hormone proteins. The common Cys amino acid residues 1–6 were labelled using black rectangles. The numbers indicated numbers of amino acid residues. (C) Reference human GHA1 protein primary structure. The 4 invariant amino acid sites were shown using white letters on black backgrounds and 13 forward amino acid sites were shown using white letters on grey backgrounds. The common Cys amino acid residues 1–6 were labelled below reference protein amino acid sequence, as well as 14 predicted functional amino acid residues (#) [9]. The α-helical regions of human GHA1 tertiary structure 1N9D were labelled by rectangles [9]. The tertiary structure determinant amino acid sites H75 and H88 were indicated by arrows [10]. The predicted signal peptide cleavage site was indicated by black triangle.
Mentions: The BioEdit 7.0.5.3 program was used in nucleotide and protein sequence analyses (http://www.mbio.ncsu.edu/BioEdit/bioedit.html). The NCBI's BLAST programs were used in identification of genes in eutherian genomic sequence assemblies downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/blast/ and ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/) [2], [3]. Alternatively, the Ensembl genome browser's BLAST or BLAT web tools were used in gene identifications (http://www.ensembl.org). The gene feature analyses included direct evidence of eutherian gene annotations deposited in NCBI's nr, est_human, est_mouse and est_others databases (http://www.ncbi.nlm.nih.gov). The protocol tested potential growth hormone (GH) coding sequences using tests of reliability of eutherian public genomic sequences. Using NCBI's BLAST programs and primary sequence reads deposited in NCBI's Trace Archive (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi), the first test step analysed nucleotide sequence coverage of potential coding sequences. The potential coding sequences were described as complete coding sequences in second test step only if consensus trace sequence coverage was available for every nucleotide. Alternatively, the potential coding sequences were described as putative coding sequences. Only the complete GH coding sequences were deposited in European Nucleotide Archive (http://www.ebi.ac.uk/ena/about/tpa-policy) and used in phylogenetic and protein molecular evolution analyses. In gene descriptions, the guidelines of human and mouse gene nomenclature were followed (http://www.genenames.org/about/guidelines and http://www.informatics.jax.org/mgihome/nomen/gene.shtml). There were 100 complete eutherian GH coding sequences, among 146 potential coding sequences (Fig. 1) (Supplementary data file 1). The most comprehensive third party data gene data set of eutherian GH genes annotated 15 GHA genes, 36 GHB genes, 5 GHC genes, 39 GHD genes and 5 GHE genes. The eutherian GHA genes were described as prolactin PRL orthologues, eutherian GHB genes were described as growth hormone GH orthologues and paralogues, domesticated guinea pig GHC genes were first described in present work, Ghd genes were described as prolactin paralogues in mouse and brown rat and GHE genes were described as prolactin paralogues in domestic cattle [4], [5], [6]. The masking of transposable elements using RepeatMasker version open-4.0.3 was included as preparatory step in multiple pairwise genomic sequence alignments, using default settings except simple repeats and low complexity elements were not masked (sensitive mode, cross_match version 1.080812, RepBase Update 20130422, RM database version 20130422) (http://www.repeatmasker.org/). In genomic sequence alignments, the mVISTA web tool was used, using AVID alignment program and default settings (http://genome.lbl.gov/vista/index.shtml). Using ClustalW implemented in BioEdit 7.0.5.3, the common predicted promoter genomic sequence regions were aligned at nucleotide sequence level and then manually corrected. The pairwise nucleotide sequence identities of common predicted promoter genomic sequence regions were calculated using BioEdit 7.0.5.3, and used in statistical analysis (Microsoft Office Excel). The common predicted promoter genomic sequence regions of eutherian GHA and GHB genes were described (Supplementary data file 2, Supplementary data file 3). For example, among primates, the calculated patterns of average pairwise nucleotide sequence identities of common predicted promoter genomic sequence regions exceeded empirically determined cut-offs of detection of common genomic sequence regions. Whereas the average pairwise nucleotide sequence identity of primate GHA common predicted promoter genomic sequence regions was ā = 0,872 (amax = 0,986, amin = 0,767, āad = 0,074) (Supplementary data file 2, Supplementary data file 3), average pairwise nucleotide sequence identity of primate GHB common predicted promoter genomic sequence regions was ā = 0,844 (amax = 0,989, amin = 0,252, āad = 0,111) (Supplementary data file 2, Supplementary data file 3).

Bottom Line: The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes.The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments.The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genomics, Centre of Animal Reproduction, 55 Heinzel St, Zagreb, Croatia.

ABSTRACT
Among 146 potential coding sequences, the most comprehensive eutherian growth hormone gene data set annotated 100 complete coding sequences. The eutherian comparative genomic analysis protocol first described 5 major gene clusters of eutherian growth hormone genes. The present updated gene classification and nomenclature of eutherian growth hormone genes integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis into new framework of future experiments. The curated third party data gene data set of eutherian growth hormone genes was deposited in European Nucleotide Archive under accession numbers LM644135-LM644234.

No MeSH data available.