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Genome Announcement: The Draft Genome of the Carrot Cyst Nematode Heterodera carotae

Catherine L. Wram

Catherine L. Wram

USDA-ARS Horticultural Crops Research UnitCorvallis,
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Wram, Catherine L.
, 
Cedar N. Hesse

Cedar N. Hesse

USDA-ARS Horticultural Crops Research UnitCorvallis,
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Hesse, Cedar N.
, 
Zafar A. Handoo

Zafar A. Handoo

USDA-ARS Mycology and Nematology Genetic Diversity and Biology LaboratoryBeltsville,
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Handoo, Zafar A.
, 
F. Hugo Pacheco

F. Hugo Pacheco

Servicio Agrícola y Ganadero (SAG), División de Protección Agrícola y Forestal y Red SAG de LaboratoriosSantiago, Chile
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Hugo Pacheco, F.
 and 
Inga A. Zasada

Inga A. Zasada

USDA-ARS Horticultural Crops Research UnitCorvallis,
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Zasada, Inga A.
  
May 29, 2022
Genome Announcement: The Draft Genome of the Carrot Cyst Nematode Heterodera carotae's Cover Image
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Article Category: Research Paper
Published Online: May 29, 2022
Received: Jan 21, 2022
DOI: https://doi.org/10.2478/jofnem-2022-0014
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© 2022 Catherine L. Wram et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

Figure S1

Visualization of the final Heterodera carotae genome assembly. Genome contigs were assembled from raw Illumina HiSeq3000 reads generated from H. carotae egg DNA using the assembler SPAdes. In this blobplot, assembled contigs are represented as circles with placement of circles on the x-axis reflecting that contig's proportion of GC bases and the position on the y-axis reflecting the coverage of the contig with the raw data. Contig circles are also colored based on their taxonomic identity indicated by the legend in the upper right-hand corner.
Visualization of the final Heterodera carotae genome assembly. Genome contigs were assembled from raw Illumina HiSeq3000 reads generated from H. carotae egg DNA using the assembler SPAdes. In this blobplot, assembled contigs are represented as circles with placement of circles on the x-axis reflecting that contig's proportion of GC bases and the position on the y-axis reflecting the coverage of the contig with the raw data. Contig circles are also colored based on their taxonomic identity indicated by the legend in the upper right-hand corner.

Figure S2

Venn diagram of complete BUSCO genes across Heterodera glycines, H. carotae, and H. schachtii. A BUSCO gene was counted as complete if denoted in the BUSCO analysis results as either complete or duplicated.
Venn diagram of complete BUSCO genes across Heterodera glycines, H. carotae, and H. schachtii. A BUSCO gene was counted as complete if denoted in the BUSCO analysis results as either complete or duplicated.

Figure S3

Phylogenetic tree of Chilean Heterodera carotae Cyclooxygenase 1 (coxI) gene in relation to other Heterodera species. The Chilean H. carotae coxI gene was extracted from the final assembly and aligned with all available coxI sequences on NCBI for H. carotae and H. cruciferae, a random selection of coxI accessions from thirty-one other Heterodera species, and five accessions of coxI from Meloidogyne species as an outgroup. A Newick phylogenetic tree was generated from the alignment. Bootstrap values are indicated on branch points in this tree and the placement within the tree of H. carotae coxI from this study highlighted in red. NCBI accessions for the sequence used are listed next to each species in the tree.
Phylogenetic tree of Chilean Heterodera carotae Cyclooxygenase 1 (coxI) gene in relation to other Heterodera species. The Chilean H. carotae coxI gene was extracted from the final assembly and aligned with all available coxI sequences on NCBI for H. carotae and H. cruciferae, a random selection of coxI accessions from thirty-one other Heterodera species, and five accessions of coxI from Meloidogyne species as an outgroup. A Newick phylogenetic tree was generated from the alignment. Bootstrap values are indicated on branch points in this tree and the placement within the tree of H. carotae coxI from this study highlighted in red. NCBI accessions for the sequence used are listed next to each species in the tree.

Figure S4

Phylogenetic tree of Chilean Heterodera carotae heat shock protein 90 (hsp90) gene in relation to other Heterodera species. The Chilean H. carotae hsp90 gene was extracted from the final assembly and aligned with hsp90 sequences from NCBI of four Globodera species, six Heterodera species, all available H. carotae accessions, two Cactodera species, and six Meloidogyne species as an outgroup. A Newick phylogenetic tree was generated from the alignment. Bootstrap values are indicated on branch points in this tree and the placement within the tree of H. carotae hsp90 from this study is highlighted in red. NCBI accessions for the sequence used are listed next to each species in the tree.
Phylogenetic tree of Chilean Heterodera carotae heat shock protein 90 (hsp90) gene in relation to other Heterodera species. The Chilean H. carotae hsp90 gene was extracted from the final assembly and aligned with hsp90 sequences from NCBI of four Globodera species, six Heterodera species, all available H. carotae accessions, two Cactodera species, and six Meloidogyne species as an outgroup. A Newick phylogenetic tree was generated from the alignment. Bootstrap values are indicated on branch points in this tree and the placement within the tree of H. carotae hsp90 from this study is highlighted in red. NCBI accessions for the sequence used are listed next to each species in the tree.

Comparison of the genome assembly statistic of Heterodera species_

Assembly statistic H. glycines (PRJNA381081)a H. schachtii (PRJNA722882)a H. carotae (PRJNA774818)a
Size (bp) 157,978,452 179,246,932 95,118,078
Number of scaffolds 9 395 17,839
Largest scaffold (bp) 23,985,585 6,046,013 113,425
GC content (%) 36.66 33.23 39.39
N50 value (bp) 17,907,690 1,273,070 13,935
No. contigs >5,000 bp 9 395 5,030
No. contigs >10,000 bp 9 359 2,755
No. contigs >25,000 bp 9 309 699
No. contigs >50,000 bp 9 269 103
Complete BUSCOs (%) 1,400 (44.7) 1,422 (45.4) 1,259 (40.2)
Complete and single-copy BUSCOs (%) 1,291 (41.2) 1,372 (43.8) 1,238 (39.5)
Complete and duplicated BUSCOs (%) 109 (3.5) 50 (1.6) 21 (0.7)
Fragmented BUSCOs (%) 109 (3.5) 120 (3.8) 143 (4.6)
Missing BUSCOs (%) 1,622 (51.8) 1,589 (50.8) 1,729 (55.2)
Predicted protein coding genes 29,679 26,768 17,212
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