Possible stochastic sex determination in Bursaphelenchus nematodes

Shinya, Ryoji; Sun, Simo; Dayı, Mehmet; Tsai, Isheng Jason; Miyama, Atsushi; Chen, Anthony Fu; Hasegawa, Koichi; Antoshechkin, Igor; Kikuchi, Taisei; Sternberg, Paul W.

doi:10.1038/s41467-022-30173-2

Cited by 17 publications

(11 citation statements)

References 70 publications

(81 reference statements)

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“…The above observation is supported by the underlying genome organization of P. scribneri containing a fair amount of gene duplication. This study suggests a diploid genome for P. scribneri which is consistent with ploidy estimations of another migratory endoparasitic nematode, B. xylophilus [ 27 ]. Further studies on comparative and functional genomics analysis are needed to validate these results and take a deeper look into the common genes and their functions between the two species.…”

Section: Discussionsupporting

confidence: 86%

First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

Arora

Hernandez

Walden

et al. 2023

IJMS

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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.

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Section: Discussionsupporting

confidence: 86%

First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

Arora

Hernandez

Walden

et al. 2023

IJMS

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“…3b ). The majority of the ancestral sex chromosomes were unambiguously assigned to chr 2, and remapping of male sequences showed equal coverage along the chromosomes ( supplementary figure S7 ), suggesting that the Aphelenchoidea superfamily including A. besseyi exhibited a stochastic sex determination system that was recently characterized in B. xylophilus 42 . Within the A. besseyi species complex, a total of 91% and 88% of genomes were in synteny between APVT and AORT, respectively.…”

Section: Resultsmentioning

confidence: 95%

TheAphelenchoidesgenomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes

Lai

Lee

et al. 2022

Preprint

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Aphelenchoides besseyi is a plant-parasitic nematode (PPN) in the Aphelenchoididae family capable of infecting more than 200 plants. A. besseyi is also a species complex with strains exhibiting varying pathogenicity to plants. We present the genome and annotations of six Aphelenchoides species, four of which belonged to the A. besseyi species complex. Most Aphelenchoides have a genome size of 44.7-47.4 Mb and are amongst the smallest in the clade IV, with the exception of A. fujianensis, which has a size of 143.8 Mb and is the largest. Phylogenomic analysis successfully delimited the species complex into A. oryzae and A. pseudobesseyi and revealed a reduction of transposon elements in the last common ancestor of Aphelenchoides. Synteny analyses between reference genomes indicated that three chromosomes in A. besseyi were derived from fission and fusion events. A systematic identification of horizontal gene transfer (HGT) genes across 27 representative nematodes allowed us to identify two major episodes of acquisition corresponding to the last common ancestor of clade IV or major PPNs, respectively. These genes were mostly lost and differentially retained between clades or strains. Most HGT events were acquired from bacteria, followed by fungi, and also from plants which was especially prevalent in Bursaphelenchus mucronatus. Our results establish a comprehensive understanding on new origins of horizontal gene transfer in nematodes.

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“…With the new chromosome-level assemblies, we have confirmed this and further obtained a much clearer view of chromosome rearrangements and fusions. The results of the new assembly clearly show that intra-chromosomal rearrangements are very frequent in the Strongyloides clade compared to other nematode groups such as the genera Caenorhabditis [44], Pristionchus [40] and Bursaphelenchus [11], which somewhat maintain synteny blocks between distantly related species, although comparisons have not been made quantitatively. Another genomic feature of this group is likely to be occasional chromosome fusions.…”

Section: Discussionmentioning

confidence: 99%

Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies

Kounosu,

Sun,

Maeda

et al. 2023

Phil. Trans. R. Soc. B

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The Strongyloides clade, to which the parasitic nematode genus Strongyloides belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites. Reproductive strategies are also diverse in this group of nematodes, employing not only sexual reproduction but also parthenogenesis, making it an attractive group to study genome adaptation to specific conditions. An in-depth understanding of genome evolution, however, has been hampered by fragmented genome assemblies. In this study, we generated chromosome-level genome assemblies for two Strongyloides species and the outgroup species Rhabditophanes diutinus using long-read sequencing and high‐throughput chromosome conformation capture (Hi-C). Our synteny analyses revealed a clearer picture of chromosome evolution in this group, suggesting that a functional sex chromosome has been maintained throughout the group. We further investigated sex chromosome dynamics in the lifecycle of Strongyloides ratti and found that bivalent formation in oocytes appears to be important for male production in the mitotic parthenogenesis. This article is part of the Theo Murphy meeting issue ‘ Strongyloides : omics to worm-free populations’.

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Possible stochastic sex determination in Bursaphelenchus nematodes

Cited by 17 publications

References 70 publications

First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

First Draft Genome Assembly of Root-Lesion Nematode Pratylenchus scribneri Generated Using Long-Read Sequencing

TheAphelenchoidesgenomes reveal substantial horizontal gene transfers in the last common ancestor of free-living and major plant parasitic nematodes

Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies

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