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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ftdoajarticles:oai:doaj.org/article:14ece4f7b5fd4094bbb14ea7b44710e4 2023-11-12T04:23:57+01:00 Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris Nazima Habibi Saif Uddin Montaha Behebehani Mohd Wasif Khan Nasreem Abdul Razzack Faiz Shirshikhar 2023-10-01T00:00:00Z https://doi.org/10.1016/j.dib.2023.109449 https://doaj.org/article/14ece4f7b5fd4094bbb14ea7b44710e4 EN eng Elsevier http://www.sciencedirect.com/science/article/pii/S2352340923005498 https://doaj.org/toc/2352-3409 2352-3409 doi:10.1016/j.dib.2023.109449 https://doaj.org/article/14ece4f7b5fd4094bbb14ea7b44710e4 Data in Brief, Vol 50, Iss , Pp 109449- (2023) Transcriptome Single nucleotide polymorphism Simple sequence repeat Indels Primers Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390 article 2023 ftdoajarticles https://doi.org/10.1016/j.dib.2023.109449 2023-10-15T00:35:54Z 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. Article in Journal/Newspaper Ocean acidification Copepods Directory of Open Access Journals: DOAJ Articles Data in Brief 50 109449 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
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language |
English |
topic |
Transcriptome Single nucleotide polymorphism Simple sequence repeat Indels Primers Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390 |
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Transcriptome Single nucleotide polymorphism Simple sequence repeat Indels Primers Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390 Nazima Habibi Saif Uddin Montaha Behebehani Mohd Wasif Khan Nasreem Abdul Razzack Faiz Shirshikhar Data on SSR markers and SNPs filtered from transcriptome of Parvocalanus crassirostris |
topic_facet |
Transcriptome Single nucleotide polymorphism Simple sequence repeat Indels Primers Computer applications to medicine. Medical informatics R858-859.7 Science (General) Q1-390 |
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 |
Article in Journal/Newspaper |
author |
Nazima Habibi Saif Uddin Montaha Behebehani Mohd Wasif Khan Nasreem Abdul Razzack Faiz Shirshikhar |
author_facet |
Nazima Habibi Saif Uddin Montaha Behebehani Mohd Wasif Khan Nasreem Abdul Razzack Faiz Shirshikhar |
author_sort |
Nazima Habibi |
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 |
https://doi.org/10.1016/j.dib.2023.109449 https://doaj.org/article/14ece4f7b5fd4094bbb14ea7b44710e4 |
genre |
Ocean acidification Copepods |
genre_facet |
Ocean acidification Copepods |
op_source |
Data in Brief, Vol 50, Iss , Pp 109449- (2023) |
op_relation |
http://www.sciencedirect.com/science/article/pii/S2352340923005498 https://doaj.org/toc/2352-3409 2352-3409 doi:10.1016/j.dib.2023.109449 https://doaj.org/article/14ece4f7b5fd4094bbb14ea7b44710e4 |
op_doi |
https://doi.org/10.1016/j.dib.2023.109449 |
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Data in Brief |
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109449 |
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