Cloning and characterization of histone H3 and replacement histone H3.3 encoding genes of Manila clam (Ruditapes philippinarum)

A full-length cDNA (rp-h3.3) encoding a replacement histone H3.3 had been identified in Manila clam (Ruditapes philippinarum). The cDNA consisted of 975 bp, including a ORF 411 bp in length, a 3′ untranslated regions 490 bp in length, a poly (A) tail and two polyadenylation signals. In addition, the cDNA encoded a peptide with the S.//.A.IG amino acid motif, which was identical to the replacement histone H3.3 variant. rpg-h3.3 and rp-h3s two sequences were obtained by amplifying the genomic DNA of R. philippinarum. The rpg-h3.3, which was the genomic DNA sequence of rp-h3.3, had one intron and the rp-h3s had no intron. It was predicted that h3s might be the h3l-like gene of R. philippinarum. Histone h3 (rp-h3) was also cloned from R. philippinarum genomic DNA. Therefore, the evolutionary origin between histone h3 and its replacement subtypes was analyzed. The study inclined to the viewpoint that h3l-like was the ancesteral gene of h3 and h3.3, which might be two different offsets from h3l-like. During histone evolution process, one copy of h3l-like genes became h3.3 by introns insertion and S-phase-coupled regulatory mechanisms lose, another copy became h3 by gene-duplication and accumulation of mutations in the S.//.A.IG motif.