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Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta)
Gracilariopsis lemaneiformis is an important commercial macroalga. Whole-genome resequencing was conducted to identify single nucleotide polymorphisms (SNPs) in parental gametophytes and 60 F(1) gametophytes of Gp. lemaneiformis in this study, and 9,989 SNPs located in nonrepetitive sequences were o...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6915112/ https://www.ncbi.nlm.nih.gov/pubmed/31921299 http://dx.doi.org/10.3389/fgene.2019.01256 |
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author | Hu, Yiyi Sui, Zhenghong Zhou, Wei Wang, Jinguo Jiang, Minjie Chen, Haihong Zhang, Jingyu Zhang, Wei Feng, Xiaoqing Lei, Yuehua Xiao, Baoheng Guo, Peng |
author_facet | Hu, Yiyi Sui, Zhenghong Zhou, Wei Wang, Jinguo Jiang, Minjie Chen, Haihong Zhang, Jingyu Zhang, Wei Feng, Xiaoqing Lei, Yuehua Xiao, Baoheng Guo, Peng |
author_sort | Hu, Yiyi |
collection | PubMed |
description | Gracilariopsis lemaneiformis is an important commercial macroalga. Whole-genome resequencing was conducted to identify single nucleotide polymorphisms (SNPs) in parental gametophytes and 60 F(1) gametophytes of Gp. lemaneiformis in this study, and 9,989 SNPs located in nonrepetitive sequences were obtained. Among these SNPs, 92.02% of loci were identified as having a heterozygous genotype in at least one gametophyte, and 48.07% of loci had identical heterozygous genotypes in the 62 gametophytes. For each gametophyte, the proportions of homozygous and heterozygous loci ranged between 13.74 and 21.61% (mean of 17.04%) and between 66.36 and 83.59% (mean of 77.12%), respectively. The remainder were missing loci, representing an average 5.84%. Sources of heterozygous SNPs were free of exogenous DNA contamination, cross contamination among individuals, plastid and mitochondrial sequences, chimeras of different thallus parts or different cells, and repetitive sequences. Genotypes of heterozygous SNPs were verified by Sanger sequencing of PCR products and monoclones. Duplications of chromosomal rearrangements in the genome of Gp. lemaneiformis might explain the presence of heterozygous SNPs in haploid gametophytes. |
format | Online Article Text |
id | pubmed-6915112 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-69151122020-01-09 Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) Hu, Yiyi Sui, Zhenghong Zhou, Wei Wang, Jinguo Jiang, Minjie Chen, Haihong Zhang, Jingyu Zhang, Wei Feng, Xiaoqing Lei, Yuehua Xiao, Baoheng Guo, Peng Front Genet Genetics Gracilariopsis lemaneiformis is an important commercial macroalga. Whole-genome resequencing was conducted to identify single nucleotide polymorphisms (SNPs) in parental gametophytes and 60 F(1) gametophytes of Gp. lemaneiformis in this study, and 9,989 SNPs located in nonrepetitive sequences were obtained. Among these SNPs, 92.02% of loci were identified as having a heterozygous genotype in at least one gametophyte, and 48.07% of loci had identical heterozygous genotypes in the 62 gametophytes. For each gametophyte, the proportions of homozygous and heterozygous loci ranged between 13.74 and 21.61% (mean of 17.04%) and between 66.36 and 83.59% (mean of 77.12%), respectively. The remainder were missing loci, representing an average 5.84%. Sources of heterozygous SNPs were free of exogenous DNA contamination, cross contamination among individuals, plastid and mitochondrial sequences, chimeras of different thallus parts or different cells, and repetitive sequences. Genotypes of heterozygous SNPs were verified by Sanger sequencing of PCR products and monoclones. Duplications of chromosomal rearrangements in the genome of Gp. lemaneiformis might explain the presence of heterozygous SNPs in haploid gametophytes. Frontiers Media S.A. 2019-12-06 /pmc/articles/PMC6915112/ /pubmed/31921299 http://dx.doi.org/10.3389/fgene.2019.01256 Text en Copyright © 2019 Hu, Sui, Zhou, Wang, Jiang, Chen, Zhang, Zhang, Feng, Lei, Xiao and Guo http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Hu, Yiyi Sui, Zhenghong Zhou, Wei Wang, Jinguo Jiang, Minjie Chen, Haihong Zhang, Jingyu Zhang, Wei Feng, Xiaoqing Lei, Yuehua Xiao, Baoheng Guo, Peng Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title | Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title_full | Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title_fullStr | Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title_full_unstemmed | Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title_short | Heterozygous Single Nucleotide Polymorphic Loci in Haploid Gametophytes of Gracilariopsis lemaneiformis (Rhodophyta) |
title_sort | heterozygous single nucleotide polymorphic loci in haploid gametophytes of gracilariopsis lemaneiformis (rhodophyta) |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6915112/ https://www.ncbi.nlm.nih.gov/pubmed/31921299 http://dx.doi.org/10.3389/fgene.2019.01256 |
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