Nematode Genome Announcement: Draft Genome of Meloidogyne chitwoodi, an Economically Important Pest of Potato in the Pacific Northwest

Abstract

Meloidogyne chitwoodi is one of the most devastating pests of potato in the U.S. Pacific Northwest (PNW). Nematode-infected tubers develop external as well as internal defects, making the potatoes unmarketable, and resulting in economic losses. Draft genome assemblies of three M. chitwoodi genotypes, Mc1, Mc2 and Mc1Roza, were generated using Illumina and PacBio Sequel RS II sequencing. The final assemblies consist of 30, 39 and 38 polished contigs for Mc1, Mc2 and Mc1Roza, respectively, with average N50 of 2.37 Mb and average assembled genome size of ~47.41 Mb. An average of 10,508 genes were annotated for each genome. BUSCO analysis indicated that 69.80% of the BUSCOs were complete whereas 68.80%, 0.93% and 12.67% were single copy, duplicated and fragmented, respectively. These highly contiguous genomes will enrich resources to study potato-nematode interactions and enhance breeding efforts to develop nematode resistant potato varieties for PNW.

Genome sequence of the coffee root-knot nematode Meloidogyne exigua

“…2C). The GC content of the assembled genome was 25.5% ( et al, 2020) and the second largest N50 length (after Meloidogyne chitwoodi; Bali et al, 2021). This reference will assist a range of genetic, genomic, and phylogenetic studies to uncover diversity and evolution of M. exigua and other related RKNs.…”

“…The quality of Illumina raw reads were assessed using FastQC (Andrews, 2010). Spades v.3.14.1 (Bankevich et al, 2012) and Blobtools v.2.1 (Kumar et al, 2013) were used to identify possible contamination; however, no potential contamination was detected. The Skewerv.0.2.2 software (Jiang et al, 2014) was used to trim reads using a minimum quality score of 30 and a minimum read length of 51 bp.…”

“…Besides, the genome assembly was 89.4% complete based on the eukaryote set ( n = 303) of Benchmarking Universal Single-Copy Orthologs (BUSCO v.3.0.2) ( Simão et al, 2015 ). Among available Meloidogyne genomes, this new assembly yields the second highest BUSCO completeness (after Meloidogyne javanica , summarized in Koutsovoulos et al, 2020 ) and the second largest N50 length (after Meloidogyne chitwoodi ; Bali et al, 2021 ). This reference will assist a range of genetic, genomic, and phylogenetic studies to uncover diversity and evolution of M. exigua and other related RKNs.…”

Understanding Molecular Plant–Nematode Interactions to Develop Alternative Approaches for Nematode Control

“…In this respect, both the comprehensive secretome (different molecular proteins secreted via the nematode stylet that is repeatedly thrust into the cells of the plant roots) profiles and the whole-genome sequence of economically important PPN species have attained significant progress for important PPN species. For example, high-quality genome sequences of serious PPN species such as major RKN species [14,[74][75][76] as well as less distributed ones, e.g., Meloidogyne luci [77], M. enterolobii [78], M. exigua [79], M. chitwoodi [80], and M. graminicola [81] are now available. Their availability should be harnessed not only to facilitate better comparative studies and phylogenomics on the related species but also help to recognize genomic variabilities and their main role in adaptability against different environmental factors and plant hosts, via examining the functional genomics.…”

Transcriptome Analyses of Pre-parasitic and Parasitic Meloidogyne Chitwoodi Race 1 to Identify Putative Effector Genes

“…The trimmed sequences were evaluated according to the summary output of FastQC, and threshold of per base sequence quality was set as 20 by default. The trimmed data was analyzed using Tophat/2.1.1 to map to the M. chitwoodi race 1 draft genome (Bali et al, 2021). Mapped read counts were calculated using Cuffdiff of the Cufflinksv2.2.1 package, and the gene read counts were converted to tab-delimited text file (Trapnell et al, 2012).…”