The complete mitochondrial genome of Kele pig (Sus scrofa) using next-generation deep sequencing

Tan, Yimin; Shi, Kaizhi; Wang, Jing; Du, Chunlin; Zhao, Chunping; Zhang, Xiong; Zhu, Li; Yi-shun, Shang

doi:10.1007/s12686-017-0797-y

Cited by 3 publications

(2 citation statements)

References 14 publications

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“…The mitochondrion contains hundreds of mitochondrial genome copies [2], which are, in contrast to the biparentally inherited nuclear genome, strictly maternally inherited. With NGS data, complete mitogenomes have been obtained for many vertebrate species, including pigs [3][4][5][6], chickens [7][8][9] and cattle [10][11][12]. It has been reported that the reference sequences used affect the accuracy of genome mapping [13][14][15].…”

Section: Introductionmentioning

confidence: 99%

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

et al. 2021

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Background Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. In this study, we used three different types of reference sequences for mitogenome mapping, i.e., the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref), respectively, and compared the accuracy of mitogenome alignment and SNP calling among them, for the purpose of proposing the optimal reference sequence for mitochondrial DNA (mtDNA) analyses of specific populations Results Four pigs, representing three different breeds, were high-throughput sequenced, subsequently mapping reads to the reference sequences mentioned above, resulting in a largest mapping ratio and a deepest coverage without increased running time when aligning reads to a BS-ref. Next, single nucleotide polymorphism (SNP) calling was carried out by 18 detection strategies with the three tools SAMtools, VarScan and GATK with different parameters, using the bam results mapping to BS-ref. The results showed that all eighteen strategies achieved the same high specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref because of a low requirement for SNP calling tools and parameter choices. Conclusions This study showed that different reference sequences representing different genetic relationships to sample reads influenced mitogenome alignment, with the breed-specific reference sequences being optimal for mitogenome analyses, which provides a refined processing perspective for NGS data.

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Section: Introductionmentioning

confidence: 99%

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

et al. 2021

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“…The mitochondrion contains hundreds of innate DNAs [2], which permits high read depths and makes mitogenome alignment from NGS data indeed feasible. With NGS data, the complete mitogenomes of many mammals have been obtained, including pigs [3][4][5][6], chickens [7][8][9] and cattle [10][11][12][13]. It is reported that reference sequences affected the accuracy in genome mapping [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Breed-specific Reference Sequence Optimizes Mapping Accuracy of NGS Analyses for Pigs

Wang

Liu

Ning

et al. 2020

Preprint

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Background: The reference sequence plays a key role in next-generation sequencing (NGS), which impacts the mapping quality during genome analyses. Especially for mitochondrion which contains plentiful amounts of innate DNA, the optimal reference sequence makes mitochondrial genome (mitogenome) alignment accurate and efficient. In this study, different mapping reference sequences, the commonly used reference sequence (CU-ref), the breed-specific reference sequence (BS-ref) and the sample-specific reference sequence (SS-ref) were compared to test the accuracy of mapping quality in the NGS analyses of pigs.Results: Four pigs from three breeds were high-throughput sequenced and subsequently mapped using three different reference mentioned above, which indicated that the BS-ref produced the largest number of mappable reads and coverages at acceptable run-times. After that, the SNP calling accuracy was evaluated by 18 detection strategies with three tools SAMtools, VarScan and GATK with different parameters under the BS-ref mapping strategy. Results showed that nine detection strategies achieved the same best specificity and sensitivity, which suggested a high accuracy of mitogenome alignment by the BS-ref alignment strategy, with a low requirement for SNP calling tools and parameter choices. Conclusions: Overall, using the breed-specific reference sequences in NGS analyses optimized the mapping quality and the SNP calling accuracy. This study indicates that the different reference sequences which represent different genetic distances between reference sequences and samples in mitogenome alignments influence alignment quality.

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Extraction and identification of bioactive peptides from Panxian dry-cured ham with multifunctional activities

Wan

et al. 2022

LWT

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The complete mitochondrial genome of Kele pig (Sus scrofa) using next-generation deep sequencing

Cited by 3 publications

References 14 publications

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

Breed-specific Reference Sequence Optimizes Mapping Accuracy of NGS Analyses for Pigs

Extraction and identification of bioactive peptides from Panxian dry-cured ham with multifunctional activities

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