Characterization of Histone Genes from the Bivalve Lucina Pectinata

Abstract

Lucina pectinata is a clam that lives in sulfide-rich environments and houses intracellular sulfide-oxidizing endosymbionts. To identify new Lucina pectinata proteins, we produced libraries for genome and transcriptome sequencing and assembled them de novo. We searched for histone-like sequences using the Lucina pectinata histone H3 partial nucleotide sequence against our previously described genome assembly to obtain the complete coding region and identify H3 coding sequences from mollusk sequences in Genbank. Solen marginatus histone nucleotide sequences were used as query sequences using the genome and transcriptome assemblies to identify the Lucina pectinata H1, H2A, H2B and H4 genes and mRNAs and obtained the complete coding regions of the five histone genes by RT-PCR combined with automated Sanger DNA sequencing. The amino acid sequence conservation between the Lucina pectinata and Solen marginatus histones was: 77%, 93%, 83%, 96% and 97% for H1, H2A, H2B, H3 and H4, respectively. As expected, the H3 and H4 proteins were the most conserved and the H1 proteins were most similar to H1′s from aquatic organisms like Crassostrea gigas, Aplysia californica, Mytilus trossulus and Biomphalaria glabrata. The Lucina pectinata draft genome and transcriptome assemblies, obtained by semiconductor sequencing, were adequate for identification of conserved proteins as evidenced by our results for the histone genes.

Does the egg capsule protect against chronic UV-B radiation? A study based on encapsulated and decapsulated embryos of cuttlefish Sepia officinalis

“…The eggs are attached to natural or artificial support in the intertidal area, where they are subject at low tide to large variations in temperature, low humidity and high amounts of sunshine (irradiance). The embryonic development of S. officinalisis within the egg involves 30 developmental stages grouped into five different phases: cleavage (stages 1-9), gastrulation (stages 10-13), organogenesis, flat stage (stages 14-18), organogenesis, extension stage (stages [19][20][21][22] and organogenesis, growth stage (stages [23][24][25][26][27][28][29][30] when the embryo has the general adult conformation [9]. The light sensitivity of S. officinalis has been demonstrated in the later stages [growth stage (stages [23][24][25][26][27][28][29][30]] of development [10,11].…”

“…The embryonic development of S. officinalisis within the egg involves 30 developmental stages grouped into five different phases: cleavage (stages 1-9), gastrulation (stages 10-13), organogenesis, flat stage (stages 14-18), organogenesis, extension stage (stages [19][20][21][22] and organogenesis, growth stage (stages [23][24][25][26][27][28][29][30] when the embryo has the general adult conformation [9]. The light sensitivity of S. officinalis has been demonstrated in the later stages [growth stage (stages [23][24][25][26][27][28][29][30]] of development [10,11]. Light can be life-saving and life-threatening depending on its wavelength, exposure time, and intensity.…”

“…The resulting photolesions may occur whatever the level of DNA compaction, but their frequency depends on DNA sequence and the presence of DNA-associated protein, such as nucleosomal histones (i.e. H3, H4, H2A and H2B) or transcriptions factors [ 23 , 24 ]. These photolesions trigger DNA repair mechanisms, especially the main DNA repair pathway, nucleotide excision repair (NER).…”

Genome-Wide Characterization and Analysis of Expression of the Histone Gene Family in Razor Clam, Sinonovacula constricta

“…With the completion of genome sequencing projects, investigations have been carried out to explore the histone gene family in a variety of species, such as C. farreri [25], grooved razor shell Solen marginatus [26], mediterranean mussel Mytilus galloprovincialis [1], the parasite Schistosoma japonicum [27], and the clam Lucina pectinata [28]. Studies on S. japonicum have demonstrated that there are totally 38 histone genes, and they are divided into 5 subfamilies and distributed on 25 scaffolds [27].…”