Chloroplast Genome Sequencing of Chenopodium album

Genome sequencing was performed using HiSeqX at Macrogen Inc., Korea, from the extracted DNA of the six C. album. De novo assembly with confirmation was accomplished with Velvet v1.2.10 [40 (link)] after filtering raw reads using Trimmomatic v0.33 [41 (link)]. After obtaining the first draft of the chloroplast genome sequences, gaps were filled with GapCloser v1.12 [42 (link)], and all bases from the assembled sequences were confirmed by checking each base in the alignment (tview mode in SAMtools v1.9 [43 (link)]) against the assembled chloroplast genome generated with BWA v0.7.17 [44 ]. All these processes were conducted under the environment of the Genome Information System (GeIS; http://geis.infoboss.co.kr/; Park et al., in preparation) like other Amaranthaceae chloroplast genomes assembled [38 (link), 39 (link), 45 (link)–49 (link)].

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Park J., Min J., Kim Y, & Chung Y. (2021). The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea. International Journal of Genomics, 2021, 6643444.

Publication 2021

HiSeqX

Amaranthaceae Bases sequences Chloroplast genomes Genome

Corresponding Organization : Shingyeong University

Other organizations : Sungkyunkwan University

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Variable analysis

independent variables

Genome sequencing using HiSeqX at Macrogen Inc., Korea
De novo assembly with confirmation using Velvet v1.2.10 after filtering raw reads using Trimmomatic v0.33
Filling gaps with GapCloser v1.12
Confirming all bases from the assembled sequences by checking each base in the alignment (tview mode in SAMtools v1.9) against the assembled chloroplast genome generated with BWA v0.7.17

dependent variables

Chloroplast genome sequences of six C. album

control variables

Extracted DNA of the six C. album
All these processes were conducted under the environment of the Genome Information System (GeIS)

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