Correction: OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

Zhu, Pengyuan; He, Lingyu; Li, Yaqiao; Huang, Wenpan; Feng, Xiaobing; Lin, Lin; Zhi, Qihuan; Zhang, Wenwei; Tang, Y. Tom; Geng, Chunyu; Lǚ, Zhiyuan; Xu, Xun

doi:10.1371/journal.pone.0138824

Cited by 18 publications

(15 citation statements)

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“…The coverage depth of a base in reference was measured. Based on the mapping results, the SNPs and indels of samples were called with the OTG-snpcaller [27] and UnifiedGenotyper in GATK [28], respectively.…”

Section: Variant Analysis Of Snps and Indelsmentioning

confidence: 99%

“…Based on mapping results, SNPs and indels between samples and reference were called with the OTG-snpcaller [27] and UnifiedGenotyper in GATK [28], respectively. We observed 356,378, 581,386, 582,079, and 544,689 SNPs and 222,008, 261,703, 261,989, and 255,033 indels from KF, K21, K5, and KM, respectively ( Table 4).…”

Section: Snps and Indels Between Samples And Reference Genomementioning

confidence: 99%

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Identification of Genetic Locus Underlying Easy Dehulling in Rice-Tartary for Easy Postharvest Processing of Tartary Buckwheat

Zhang

Liu

2020

Genes

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As a highly nutritious crop, Tartary buckwheat (Fagopyrum tartaricum) strongly adapts and grows in adverse environments and is widely grown in Asia. However, its flour contains a large proportion of the hull that adheres to the testa layer of the groats and is difficult to be removed in industrial processing. Fortunately, rice-Tartary, with the loose and non-adhering hull, provides potentiality of improving Tartary buckwheat that can dehull easily. Here, we performed high-throughput sequencing for two parents (Tartary buckwheat and rice-Tartary) and two pools (samples from the F2 population) and obtained 101 Gb raw sequencing data for further analysis. Sequencing reads were mapped to the reference genome of Tartary buckwheat, and a total of 633,256 unique SNPs and 270,181 unique indels were found in these four samples. Then, based on the Bulked Segregant Analysis (BSA), we identified a candidate genetic region, containing 45 impact SNPs/indels and 36 genes, that might underly non-adhering hull of rice-Tartary and should have value for breeding easy dehulling Tartary buckwheat.

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Section: Variant Analysis Of Snps and Indelsmentioning

confidence: 99%

Section: Snps and Indels Between Samples And Reference Genomementioning

confidence: 99%

Identification of Genetic Locus Underlying Easy Dehulling in Rice-Tartary for Easy Postharvest Processing of Tartary Buckwheat

Zhang

Liu

2020

Genes

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“…The genomic DNA was extracted using a genomic DNA extraction kit (Tiangen Biotech, Beijing, China), and was sequenced with both PacBio RSII and Illumina Hiseq 2000 platforms. The cleaned PacBio subreads were assembled using CANU (Koren et al 2017), and the possible sequencing errors were corrected using the Illumina Hiseq reads by softwares GATK (Zhu et al 2015). The mitochondrial genome has been deposited in the GenBank under accession number MN934958 and in the Genome Warehouse at the National Genomics Data Center (Members 2019), Beijing Institute of Genomics (BIG) under accession number GWHABJT00000000 (https://bigd.big.ac.cn/gwh).…”

Section: Heveochlorella;mentioning

confidence: 99%

The mitochondrion genome of Heveochlorella roystonensis (Trebouxiophyceae) contains large direct repeats

Han

et al. 2020

Mitochondrial DNA Part B

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The mitochondrial genome of the epiphytic green alga, Heveochlorella roystonensis was sequenced and characterized. The complete mitogenome contains 130,507 bp, including a single-copy region of 54,865 bp and two direct repeat regions of 37,816 and 37,826 bp, respectively, and has a G þ C content of 34.2%. It contains 110 genes, including 73 protein coding genes, 34 tRNA, and three rRNA genes. The large direct repeat makes it currently the largest mitochondrial genome in Trebouxiophyceae.

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“…The total genomic DNA was extracted using a genomic DNA extraction kit (Tiangen Biotech, Beijing, China), and was sequenced with both PacBio RSII and Illumina Hiseq 2000 platforms at Genoseq (Wuhan, China). The filtered reads were assembled using CANU (Koren et al 2017) and GATK (Zhu et al 2015). The mitochondrial genome was deposited in the GenBank under accession number MN966687.…”

Section: Heveochlorella;mentioning

confidence: 99%

The complete mitochondrial genome of the rubber tree endophytic alga Heveochlorella hainangensis

Han

et al. 2020

Mitochondrial DNA Part B

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Heveochlorella hainangensis is an endophytic green alga in the rubber tree. Its mitocondrion genome was sequenced and characterized. The complete mitogenome contains 54,084 bp with a G þ C content of 30.94%. It contains 56 genes, including 32 protein coding genes, 21 tRNA, and 3 rRNA genes. Phylogenetic analysis using the mitogenomes of Trebouxiophyceae species indicated that H. hainangensis is closely related to H. roystonensis, and they both clustered in the Watanabea clade.

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Correction: OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

Cited by 18 publications

References 1 publication

Identification of Genetic Locus Underlying Easy Dehulling in Rice-Tartary for Easy Postharvest Processing of Tartary Buckwheat

Identification of Genetic Locus Underlying Easy Dehulling in Rice-Tartary for Easy Postharvest Processing of Tartary Buckwheat

The mitochondrion genome of Heveochlorella roystonensis (Trebouxiophyceae) contains large direct repeats

The complete mitochondrial genome of the rubber tree endophytic alga Heveochlorella hainangensis

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