Whole-genome sequence of the planarian Dugesia japonica combining Illumina and PacBio data
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Whole-genome sequence of the planarian Dugesia japonica combining Illumina and PacBio data. / Tian, Qingnan; Guo, Qi; Guo, Yanan; Luo, Longhai; Kristiansen, Karsten; Han, Zujing; Fang, Huimin; Zhang, Shoutao.
In: Genomics, Vol. 114, No. 2, 110293, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Whole-genome sequence of the planarian Dugesia japonica combining Illumina and PacBio data
AU - Tian, Qingnan
AU - Guo, Qi
AU - Guo, Yanan
AU - Luo, Longhai
AU - Kristiansen, Karsten
AU - Han, Zujing
AU - Fang, Huimin
AU - Zhang, Shoutao
N1 - Publisher Copyright: © 2022
PY - 2022
Y1 - 2022
N2 - Advances in stem cell biology have posed the challenges in revealing the mechanistic themes underlying whole tissues and organs formation during regeneration. The planarian Dugesia japonica is an ideal model organism for the study of regeneration and stem cell biology. However, the genome resources for this species are still limited. Here, we combined single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing and 10× Genomics linked reads data to obtain the whole-genome sequence of the planarian D. japonica. The final assembled D. japonica genome is 1.13G with contig N50 of 248.44 kb, and scaffold N50 of 652.52 kb. Repeat elements account for 64.92% of the genome, and 12,031 protein coding genes were annotated, of which 10,114 genes had at least one functional annotation, representing 84.07% of the total genes. We present a highly contiguous genome assembly of D. japonica. The D. japonica genome assembly, together with gene annotation and transcriptome data provide a valuable resource to investigate molecular mechanism of planarian and stem cell research.
AB - Advances in stem cell biology have posed the challenges in revealing the mechanistic themes underlying whole tissues and organs formation during regeneration. The planarian Dugesia japonica is an ideal model organism for the study of regeneration and stem cell biology. However, the genome resources for this species are still limited. Here, we combined single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing and 10× Genomics linked reads data to obtain the whole-genome sequence of the planarian D. japonica. The final assembled D. japonica genome is 1.13G with contig N50 of 248.44 kb, and scaffold N50 of 652.52 kb. Repeat elements account for 64.92% of the genome, and 12,031 protein coding genes were annotated, of which 10,114 genes had at least one functional annotation, representing 84.07% of the total genes. We present a highly contiguous genome assembly of D. japonica. The D. japonica genome assembly, together with gene annotation and transcriptome data provide a valuable resource to investigate molecular mechanism of planarian and stem cell research.
KW - Bioinformatics
KW - D. japonica
KW - Functional annotation
KW - Planarian
KW - Whole genome sequencing
U2 - 10.1016/j.ygeno.2022.110293
DO - 10.1016/j.ygeno.2022.110293
M3 - Journal article
C2 - 35139429
AN - SCOPUS:85124486174
VL - 114
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 2
M1 - 110293
ER -
ID: 302448786