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. 2020 Aug 5;21(1):542.
doi: 10.1186/s12864-020-06958-4.

Comparative genomic analysis of eutherian fibroblast growth factor genes

Marko Premzl  1
Affiliations

Comparative genomic analysis of eutherian fibroblast growth factor genes

Marko Premzl. BMC Genomics. .

Abstract

Background: The eutherian fibroblast growth factors were implicated as key regulators in developmental processes. However, there were major disagreements in descriptions of comprehensive eutherian fibroblast growth factors gene data sets including either 18 or 22 homologues. The present analysis attempted to revise and update comprehensive eutherian fibroblast growth factor gene data sets, and address and resolve major discrepancies in their descriptions using eutherian comparative genomic analysis protocol and 35 public eutherian reference genomic sequence data sets.

Results: Among 577 potential coding sequences, the tests of reliability of eutherian public genomic sequences annotated most comprehensive curated eutherian third-party data gene data set of fibroblast growth factor genes including 267 complete coding sequences. The present study first described 8 superclusters including 22 eutherian fibroblast growth factor major gene clusters, proposing their updated classification and nomenclature.

Conclusions: The integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis argued that comprehensive eutherian fibroblast growth factor gene data set classifications included 22 rather than 18 homologues.

Keywords: Eutheria; Gene annotations; Molecular evolution; Phylogenetic analysis; RRID:SCR_014401.

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Conflict of interest statement

No competing interests were declared.

Figures

Fig. 1
Fig. 1
Phylogenetic analysis of eutherian fibroblast growth factor genes. The minimum evolution phylogenetic tree including bootstrap estimates higher than 50% after 1000 replicates was calculated using maximum composite likelihood method. The 8 major gene superclusters FGF1–8 were indicated
Fig. 2
Fig. 2
Major landmarks in eutherian fibroblast growth factor protein sequence alignments. The black squares labelled common cysteine amino acid residues. The grey squares labelled common exon-intron splice site amino acid sites. The white squares labelled common N-glycosylation sites. The numbers indicated numbers of amino acid residues
Fig. 3
Fig. 3
Tests of protein molecular evolution of eutherian fibroblast growth factors. a Relative synonymous codon usage statistics of eutherian FGF gene data set. The not preferable amino acid codons were indicated by white letters on red backgrounds. Counts, observed amino acid codon counts; R, relative synonymous codon usage statistics; &, stop codons. b Reference human FGF1A protein amino acid sequence. The 19 invariant amino acid sites were shown using white letters on violet backgrounds. Whereas the 5 amino acid sites that were invariant among 22 FGF major protein clusters were indicated by black arrows (except that M1 was invariant among 266 FGF protein primary structures), grey arrows indicated 2 amino acid sites that were invariant among 21 FGF major protein clusters respectively. The 3 forward amino acid sites were shown using white letters on red backgrounds. The stars labelled 2 forward amino acid sites described among 22 FGF major protein clusters. The positions of 12 β-strands implicated in β-trefoil protein tertiary structure were indicated below reference human FGF1A protein primary structure [22, 24]
Fig. 4
Fig. 4
Eutherian comparative genomic analysis protocol flowchart
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