Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris
Calanoid copepod populations are being severely affected due to the effects of ocean acidification (OA) and ocean warming (OW). These marine organisms are the most abundant primary consumers contributing significantly in the marine food web. Any effect on the abundance and diversity of copepods due...
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ftpubmed:oai:pubmedcentral.nih.gov:10430150 2023-09-05T13:22:14+02:00 Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris Habibi, Nazima Uddin, Saif Behebehani, Montaha Khan, Mohd Wasif Razzack, Nasreem Abdul Shirshikhar, Faiz 2023-07-28 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10430150/ https://doi.org/10.1016/j.dib.2023.109449 en eng Elsevier http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10430150/ http://dx.doi.org/10.1016/j.dib.2023.109449 © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Data Brief Data Article Text 2023 ftpubmed https://doi.org/10.1016/j.dib.2023.109449 2023-08-20T01:05:09Z Calanoid copepod populations are being severely affected due to the effects of ocean acidification (OA) and ocean warming (OW). These marine organisms are the most abundant primary consumers contributing significantly in the marine food web. Any effect on the abundance and diversity of copepods due to climate change is likely to have serious implications on the marine ecosystem functioning. Molecular studies that play a vital role in assessing the genetic changes under the influence of environmental imbalances are completely lacking for this species. Here we report the genetic variations in three generations of copepods through transcriptome sequencing. RNA sequencing was performed on an Illumina HiSeq platform employing the 2 × 100 bp paired-end chemistry. Approximately, 10GB of data was obtained for all the samples. The raw sequences were assembled through Trinity 2.6.6 and mined for single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). MIcroSAtellite Identification Tool (MISA) was used for SSR detection and Primer 3 (v 3.0) was utilized to design short oligonucleotide primers (18-20 mers). A total of 15,222 SSRs were identified and 28,944 primer pairs were designed against these motifs. The transcriptome possessed 413,890 SNPs at a frequency of 2.8 per kb. The newly discovered SSRs and SNPs could act as genetic markers for future studies on genetic diversity and conservation for Parvocalanus crassirostris. Text Ocean acidification Copepods PubMed Central (PMC) Data in Brief 50 109449 |
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Data Article Habibi, Nazima Uddin, Saif Behebehani, Montaha Khan, Mohd Wasif Razzack, Nasreem Abdul Shirshikhar, Faiz Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
topic_facet |
Data Article |
description |
Calanoid copepod populations are being severely affected due to the effects of ocean acidification (OA) and ocean warming (OW). These marine organisms are the most abundant primary consumers contributing significantly in the marine food web. Any effect on the abundance and diversity of copepods due to climate change is likely to have serious implications on the marine ecosystem functioning. Molecular studies that play a vital role in assessing the genetic changes under the influence of environmental imbalances are completely lacking for this species. Here we report the genetic variations in three generations of copepods through transcriptome sequencing. RNA sequencing was performed on an Illumina HiSeq platform employing the 2 × 100 bp paired-end chemistry. Approximately, 10GB of data was obtained for all the samples. The raw sequences were assembled through Trinity 2.6.6 and mined for single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). MIcroSAtellite Identification Tool (MISA) was used for SSR detection and Primer 3 (v 3.0) was utilized to design short oligonucleotide primers (18-20 mers). A total of 15,222 SSRs were identified and 28,944 primer pairs were designed against these motifs. The transcriptome possessed 413,890 SNPs at a frequency of 2.8 per kb. The newly discovered SSRs and SNPs could act as genetic markers for future studies on genetic diversity and conservation for Parvocalanus crassirostris. |
format |
Text |
author |
Habibi, Nazima Uddin, Saif Behebehani, Montaha Khan, Mohd Wasif Razzack, Nasreem Abdul Shirshikhar, Faiz |
author_facet |
Habibi, Nazima Uddin, Saif Behebehani, Montaha Khan, Mohd Wasif Razzack, Nasreem Abdul Shirshikhar, Faiz |
author_sort |
Habibi, Nazima |
title |
Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
title_short |
Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
title_full |
Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
title_fullStr |
Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
title_full_unstemmed |
Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
title_sort |
data on ssr markers and snps filtered from transcriptome of parvocalanus crassirostris |
publisher |
Elsevier |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10430150/ https://doi.org/10.1016/j.dib.2023.109449 |
genre |
Ocean acidification Copepods |
genre_facet |
Ocean acidification Copepods |
op_source |
Data Brief |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10430150/ http://dx.doi.org/10.1016/j.dib.2023.109449 |
op_rights |
© 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
op_doi |
https://doi.org/10.1016/j.dib.2023.109449 |
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