Characterization of Histone Genes from the Bivalve Lucina Pectinata
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 usi...
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ftdoajarticles:oai:doaj.org/article:5162a22c2a97460893135398e213bd1e 2023-05-15T15:58:46+02:00 Characterization of Histone Genes from the Bivalve Lucina Pectinata Ingrid M. Montes-Rodríguez Yesenia Rodríguez-Pou Ricardo R. González-Méndez Juan Lopez-Garriga Alexander J. Ropelewski Carmen L. Cadilla 2018-10-01T00:00:00Z https://doi.org/10.3390/ijerph15102170 https://doaj.org/article/5162a22c2a97460893135398e213bd1e EN eng MDPI AG http://www.mdpi.com/1660-4601/15/10/2170 https://doaj.org/toc/1660-4601 1660-4601 doi:10.3390/ijerph15102170 https://doaj.org/article/5162a22c2a97460893135398e213bd1e International Journal of Environmental Research and Public Health, Vol 15, Iss 10, p 2170 (2018) histone gene gene variants mollusk gene evolution bioinformatics next-generation sequencing Sanger sequencing Medicine R article 2018 ftdoajarticles https://doi.org/10.3390/ijerph15102170 2022-12-31T07:19:37Z 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. Article in Journal/Newspaper Crassostrea gigas Directory of Open Access Journals: DOAJ Articles International Journal of Environmental Research and Public Health 15 10 2170 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
histone gene gene variants mollusk gene evolution bioinformatics next-generation sequencing Sanger sequencing Medicine R |
spellingShingle |
histone gene gene variants mollusk gene evolution bioinformatics next-generation sequencing Sanger sequencing Medicine R Ingrid M. Montes-Rodríguez Yesenia Rodríguez-Pou Ricardo R. González-Méndez Juan Lopez-Garriga Alexander J. Ropelewski Carmen L. Cadilla Characterization of Histone Genes from the Bivalve Lucina Pectinata |
topic_facet |
histone gene gene variants mollusk gene evolution bioinformatics next-generation sequencing Sanger sequencing Medicine R |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Ingrid M. Montes-Rodríguez Yesenia Rodríguez-Pou Ricardo R. González-Méndez Juan Lopez-Garriga Alexander J. Ropelewski Carmen L. Cadilla |
author_facet |
Ingrid M. Montes-Rodríguez Yesenia Rodríguez-Pou Ricardo R. González-Méndez Juan Lopez-Garriga Alexander J. Ropelewski Carmen L. Cadilla |
author_sort |
Ingrid M. Montes-Rodríguez |
title |
Characterization of Histone Genes from the Bivalve Lucina Pectinata |
title_short |
Characterization of Histone Genes from the Bivalve Lucina Pectinata |
title_full |
Characterization of Histone Genes from the Bivalve Lucina Pectinata |
title_fullStr |
Characterization of Histone Genes from the Bivalve Lucina Pectinata |
title_full_unstemmed |
Characterization of Histone Genes from the Bivalve Lucina Pectinata |
title_sort |
characterization of histone genes from the bivalve lucina pectinata |
publisher |
MDPI AG |
publishDate |
2018 |
url |
https://doi.org/10.3390/ijerph15102170 https://doaj.org/article/5162a22c2a97460893135398e213bd1e |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
International Journal of Environmental Research and Public Health, Vol 15, Iss 10, p 2170 (2018) |
op_relation |
http://www.mdpi.com/1660-4601/15/10/2170 https://doaj.org/toc/1660-4601 1660-4601 doi:10.3390/ijerph15102170 https://doaj.org/article/5162a22c2a97460893135398e213bd1e |
op_doi |
https://doi.org/10.3390/ijerph15102170 |
container_title |
International Journal of Environmental Research and Public Health |
container_volume |
15 |
container_issue |
10 |
container_start_page |
2170 |
_version_ |
1766394537145532416 |