|
KMID : 0613820190290010001
|
|
Journal of Life Science
2019 Volume.29 No. 1 p.1 ~ p.8
|
|
|
A Comparative Analysis of the Illumina Truseq Synthetic Long-read Haplotyping Sequencing Platform versus the 10X Genomics Chromium Genome Sequencing Platform for Haplotype Phasing and the Identification of Single-nucleotide variants (SNVs) in Hanwoo (Korean Native Cattle)
|
|
Park Won-Cheoul
Krishnamoorthy Srikanth
Park Jong-Eun
Shin Dong-Hyun
Ko Hae-Su
Lim Da-Jeong
Cho In-Cheol
|
|
|
Abstract
|
|
|
|
In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using high- depth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.
|
|
|
KEYWORD
|
|
|
Hanwoo, Haplotype, SNVs, The Chromium Genome Sequencing, TSLRH Sequencing
|
|
|
FullTexts / Linksout information
|
|
|
|
|
Listed journal information
|
|
|
|