Genome Assembly and Annotation of the Alfalfa Cyst Nematode (Heterodera medicaginis)

Postnikova, Olga A.; Wram, Catherine; Grinstead, Sam; Vieira, Paulo; Nemchinov, Lev G.

doi:10.2478/jofnem-2025-0047

Figures & Tables

Example of the Heterodera medicaginis cysts with eggs extracted from the soil of infected alfalfa plants used in this study.

Visualization of the final assembly of Heterodera medicaginis. Utilizing blobtools (Laetsch and Baxter, 2017) the genome assembly was visualized with contigs represented as circles and their placement on the x and y axes reflecting GC% and contig coverage based on raw data respectively. Contig size is reflected in circle size.

Phylogenetic tree of isolate from the current study of Heterodera medicaginis cytochrome c oxidase subunit 1 (coxI) gene in relation to other Heterodera species. The coxI gene was extracted from the final assembly and aligned with two coxI sequences on NCBI for H. medicaginis, a random selection of coxI accessions from other Heterodera species, Meloidogyne species and Caenorhabditis elegans as an outgroup. A Maximum likelihood phylogenetic tree was generated from the alignment using CLC Genomic Workbench v 24. Bootstrap values (>50) are indicated on branch points in this tree and the placement within the tree of H. medicaginis coxI from this study highlighted with a red arrow. NCBI accessions for the sequence used are listed next to each species in the tree.

Phylogenetic tree of isolate from the current study of Heterodera medicaginis heat shock protein 90 (hsp90) gene in relation to other Heterodera species. The hsp90 gene was extracted from the final assembly and aligned with hsp90 sequences from NCBI of eight Heterodera species, two H. medicaginis accessions, three Meloidogyne species, and Caenorhabditis elegans as an outgroup. A Maximum likelihood phylogenetic tree was generated from the alignment using CLC Genomic Workbench v 24 with 1,000 bootstrap alignments. Bootstrap values (>50) are indicated on branch points in this tree and the placement within the tree of H. medicaginis hsp90 from this study is highlighted with a red arrow. NCBI accessions for the sequence used are listed next to each species in the tree.

Genome assembly statistics of H_ medicaginis and other Heterodera species_

*Assembly statistic*	*H. medicaginis*	H. glycines (PRJNA381081)^a	H. schachtii (PRJNA522950)^a	H. humuli (PRJNA1048471)^a	H. carotae (PRJNA774818)^a	H. filipjevi (PRJNA1113137)^a
Read type	Nanopore	PacBio/Illumina	PacBio/Illumina	PacBio	Illumina	PacBio RS/Illumina
Total length	112,910,497	157,978,452	179,246,932	90,806,450	95,115,141	134,189,547
Number of contigs/Number of Scaffolds	1,383/1,383	2,121/9	1,682/395	1,487/1,487	17,835/17,835	1,208/661
Largest contig	1,183,061	23,985,585	6,046,013	568,746	113,425	30,258,874
Number of contigs (≥25,000 bp)	927	9	309	871	699	210
Number of contigs (≥50,000 bp)	655	9	269	559	103	63
GC (%)	37	37	33	36	39	36.76
N50	148,984	17,907,690	1,273,070	111,383	13,935	11,883,475
L50	220	4	40	231	1,836	4
Number of N’s per 100 kbp	0	1,062	2,756	0	0	564.5
RNA-seq evidence used for annotation	No	Yes	Yes	No	No	Yes
Coding genes	17,779	22,465	26,739	15,428	18,781	13,352
^bCDS	20,698	23,917	32,600	16,848	20,104	13,352
Proteins	20,698	23,917	32,600	16,848	20,104	13,352
Predicted protein BUSCO analysis (Nematoda_odb10)
^cComplete BUSCOs (C)	1,757 (56.1%)	1,884 (60.2%)	2,080 (66.4%)	2,030 (64.9%)	1,301 (41.5%)	1,873 (59.8%)
Complete and single-copy BUSCOs (S)	1,696 (54.2%)	1,612 (51.5%)	1,675 (53.5%)	1,590 (50.8%)	1,237 (39.5%)	1,805 (57.6%)
Complete and duplicated BUSCOs (D)	61 (1.9%)	272 (8.7%)	405 (12.9%)	440 (14.1%)	64 (2%)	68 (2.2%)
Fragmented BUSCOs (F)	108 (3.4%)	47 (1.5%)	69 (2.2%)	66 (2.1%)	124 (4%)	102 (3.3%)
Missing BUSCOs (M)	1266 (40.5%)	1,200 (38.3%)	982 (31.4%)	1,035 (33%)	1,706 (54.5%)	1,156 (36.9%)
Total BUSCO groups searched	3,131	3,131	3,131	3,131	3,131	3,131
Predicted protein BUSCO analysis (Eukaryota_odb10)
^cComplete BUSCOs (C)	297 (77.3%)	199 (78%)	224 (87.8%)	221 (86.6%)	160 (62.8%)	205 (80.4%)
Complete and single-copy BUSCOs (S)	194 (76.1%)	176 (69%)	200 (78.4%)	174 (68.2%)	156 (61.2%)	194 (76.1%)
Complete and duplicated BUSCOs (D)	3 (1.2%)	23 (9%)	24 (9.4%)	47 (18.4%)	4 (1.6%)	11 (4.3%)
Fragmented BUSCOs (F)	20 (7.8%)	20 (7.8%)	15 (5.9%)	13 (5.1%)	52 (20.4%)	13 (5.1%)
Missing BUSCOs (M)	38 (14.9%)	36 (14.2%)	16 (6.3%)	21 (8.3%)	43 (16.8%)	37 (14.5%)
Total BUSCO groups searched	255	255	255	255	255	255

Genome Assembly and Annotation of the Alfalfa Cyst Nematode (Heterodera medicaginis)

Figures & Tables

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Genome assembly statistics of H_ medicaginis and other Heterodera species_

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