TY - JOUR
T1 - First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing
AU - Arora, Deepika
AU - Hernandez, Alvaro G.
AU - Walden, Kimberly K.O.
AU - Fields, Christopher J.
AU - Yan, Guiping
N1 - We thank the North Dakota Corn Council and the North Dakota State Board of Agricultural Research and Education for funding this project. The authors would also like to thank Ekta Ojha for her assistance in providing nematode carrot cultures for Method 1.
This research was funded by the North Dakota State Board of Agricultural Research and Education under funding number FARG090473 and the North Dakota Corn Council under funding number FAR0035599.
PY - 2023/4
Y1 - 2023/4
N2 - Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level.
AB - Root-lesion nematodes (genus Pratylenchus) belong to a diverse group of plant-parasitic nematodes (PPN) with a worldwide distribution. Despite being an economically important PPN group of more than 100 species, genome information related to Pratylenchus genus is scarcely available. Here, we report the draft genome assembly of Pratylenchus scribneri generated on the PacBio Sequel IIe System using the ultra-low DNA input HiFi sequencing workflow. The final assembly created using 500 nematodes consisted of 276 decontaminated contigs, with an average contig N50 of 1.72 Mb and an assembled draft genome size of 227.24 Mb consisting of 51,146 predicted protein sequences. The benchmarking universal single-copy ortholog (BUSCO) analysis with 3131 nematode BUSCO groups indicated that 65.4% of the BUSCOs were complete, whereas 24.0%, 41.4%, and 1.8% were single-copy, duplicated, and fragmented, respectively, and 32.8% were missing. The outputs from GenomeScope2 and Smudgeplots converged towards a diploid genome for P. scribneri. The data provided here will facilitate future studies on host plant-nematode interactions and crop protection at the molecular level.
KW - root-lesion nematode
KW - genome
KW - ultra-low DNA input
KW - contigs
KW - sequencing
KW - BUSCO
KW - diploid
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U2 - 10.3390/ijms24087311
DO - 10.3390/ijms24087311
M3 - Article
C2 - 37108472
SN - 1422-0067
VL - 24
JO - International journal of molecular sciences
JF - International journal of molecular sciences
IS - 8
M1 - 7311
ER -