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    多倍体的SNP

    植物基因组学
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    • A
      anneng 最后由 编辑

      https://sci-hub.st/10.1007/s00438-008-0365-y
      Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa

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      • A
        anneng 最后由 编辑

        https://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2011.00644.x
        8c567351-00c5-45ad-aff3-5f2944bfe732-image.png

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        • A
          anneng 最后由 编辑

          https://max.book118.com/html/2014/0318/6706569.shtm
          多倍体植物中单核苷酸多态性（SNPs）的开发

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          • A
            anneng 最后由 anneng 编辑

            https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920642/
            Homoeologs: What Are They and How Do We Infer Them?
            Homoeologs are pairs of genes that originated by speciation and were brought back together in the same genome by allopolyploidization.
            Homoeologs are not necessarily one-to-one or positionally conserved.
            部分同源指的是基因经过不同的演化后，又因为异源杂交，被放到了同一个基因组中。
            allopolyploids result from genome doubling following a hybridization between two different species (interspecific), whereas autopolyploids result from genome doubling within one species (intraspecific).

            cd057de5-8107-4caa-b112-4394e381ca7e-image.png
            a284a42b-0fd3-4721-8705-c9adfcb566c3-image.png

            473426ad-5964-486c-9918-7c5f85f0f294-image.png

            https://lab.dessimoz.org/blog/2016/03/24/what-are-homoeologs
            Last but not least, we learned that even though homoeolog has alternatively been spelled “homeolog” (no extra o), homoeolog is the clear winner in terms of popularity.
            homoeolog有时候也被写作homeolog

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            • A
              anneng 最后由 编辑

              genes-11-01220-v2.pdf
              b3e2d517-30ea-4fe1-8adc-58f82683f1d0-image.png
              这个文献研究了花生 花生也是一个异源四倍体 相似的文献可以重点看看
              这个流程结合了GATK+Sweep

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              • A
                anneng 最后由 编辑

                https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5062318/
                Conserved but Attenuated Parental Gene Expression in Allopolyploids: Constitutive Zinc Hyperaccumulation in the Allotetraploid Arabidopsis kamchatica

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                • A
                  anneng 最后由 编辑

                  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356317/
                  ba57d465-2ab9-46a9-9896-849da064666d-image.png

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                  • A
                    anneng 最后由 编辑

                    SNP Discovery in Complex Allotetraploid Genomes
                    (Gossypium spp., Malvaceae) Using Genotyping by
                    Sequencing
                    apps.1400077.pdf

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                    • A
                      anneng 最后由 编辑

                      A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
                      https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-100

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                      • A
                        anneng 最后由 anneng 编辑

                        https://api.research-repository.uwa.edu.au/ws/portalfiles/portal/57891001/THESIS_DOCTOR_OF_PHILOSOPHY_SCHEBEN_Armin_2019.pdf
                        THESIS_DOCTOR_OF_PHILOSOPHY_SCHEBEN_Armin_2019.pdf
                        这个文章里面说可以通过比对后的质量值 筛选比对到多个位置的序列

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                        • A
                          anneng 最后由 编辑

                          https://gist.github.com/sbamin/27acf13f2a28161efbf89a273559bca4
                          https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment

                          sambamba view -t 12 -h -f bam -F "mapping_quality >= 1 and not (unmapped or secondary_alignment) and not ([XA] != null or [SA] != null)" test.bwa-mem.bam -o test-uniq.bam

                          获取唯一比对的序列

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                          • A
                            anneng 最后由 编辑

                            https://www.frontiersin.org/articles/10.3389/fgene.2020.00222/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=521391

                            Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut

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                            • A
                              anneng 最后由 编辑

                              https://www.frontiersin.org/articles/10.3389/fgene.2020.00222/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=521391
                              Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut

                              该文献对异源多倍体的snp分析对比了5种流程 可以重点看看

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