- NSF-PAR ID:
- 10292923
- Date Published:
- Journal Name:
- International Journal of Molecular Sciences
- Volume:
- 22
- Issue:
- 9
- ISSN:
- 1422-0067
- Page Range / eLocation ID:
- 4326
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Background Gastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta , infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta , such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics. Results We have constructed a high-quality reference genome, with chromosome-length scaffolds, by purging alternative haplotypes from the existing draft genome assembly and scaffolding the result using chromosome conformation, capture-based, in situ Hi-C technique. The improved (Hi-C) assembly resulted in six chromosome-length scaffolds with length ranging from 66.6 Mbp to 49.6 Mbp, 35% fewer sequences and reduction in size. Substantial improvements were also achieved in both the values for N50 (57.1 Mbp) and L50 (5 Mbp). A higher and comparable level of genome and proteome completeness was achieved for Hi-C assembly on BUSCO parameters. The Hi-C assembly had a greater synteny and number of orthologs with a closely related nematode, Haemonchus contortus. Conclusion This improved genomic resource is suitable as a foundation for the identification of potential targets for vaccine and drug development.more » « less
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Summary Rhizobial lipochitooligosaccharidic Nod factors (NFs), specified by
nod genes, are the primary determinants of host specificity in the legume–Rhizobia symbiosis.We examined the nodulation ability of
Medicago truncatula cv Jemalong A17 andM. truncatula ssp.tricycla R108 with theSinorhizobium meliloti nodF/nodL mutant, which produces modified NFs. We then applied genetic and functional approaches to study the genetic basis and mechanism of nodulation of R108 by this mutant.We show that the
nodF/nodL mutant can nodulate R108 but not A17. Using genomics and reverse genetics, we identified a newly evolved, chimeric LysM receptor‐like kinase gene in R108,LYK2bis , which is responsible for the phenotype and can allow A17 to gain nodulation with thenodF/nodL mutant. We found thatLYK2bis is involved in nodulation by mutants producing nonO ‐acetylated NFs and interacts with the key receptor protein NFP. Many, but not all, naturalS. meliloti andS. medicae strains tested requireLYK2bis for efficient nodulation of R108.Our findings reveal that a newly evolved gene in R108,
LYK2bis , extends nodulation specificity to mutants producing nonO ‐acetylated NFs and is important for nodulation by many naturalSinorhizobia . Evolution of this gene may present an adaptive advantage to allow nodulation by a greater variety of strains. -
SUMMARY Medicago truncatula is a model legume for fundamental research on legume biology and symbiotic nitrogen fixation.Tnt1 , a retrotransposon from tobacco, was used to generate insertion mutants inM. truncatula R108. Approximately 21 000 insertion lines have been generated and publicly available.Tnt1 retro‐transposition event occurs during somatic embryogenesis (SE), a pivotal process that triggers massive methylation changes. We studied the SE ofM. truncatula R108 using leaf explants and explored the dynamic shifts in the methylation landscape from leaf explants to callus formation and finally embryogenesis. Higher cytosine methylation in all three contexts of CG, CHG, and CHH patterns was observed during SE compared to the controls. Higher methylation patterns were observed in assumed promoter regions (~2‐kb upstream regions of transcription start site) of the genes, while lowest was recorded in the untranslated regions. Differentially methylated promoter region analysis showed a higher CHH methylation in embryogenesis tissue samples when compared to CG and CHG methylation. Strong correlation (89.71%) was identified between the differentially methylated regions (DMRs) and the site ofTnt1 insertions inM. truncatula R108 and stronger hypermethylation of genes correlated with higher number ofTnt1 insertions in all contexts of CG, CHG, and CHH methylation. Gene ontology enrichment and KEGG pathway enrichment analysis identified genes and pathways enriched in the signal peptide processing, ATP hydrolysis, RNA polymerase activity, transport, secondary metabolites, and nitrogen metabolism pathways. Combined gene expression analysis and methylation profiling showed an inverse relationship between methylation in the DMRs (regions spanning genes) and the expression of genes. Our results show that a dynamic shift in methylation happens during the SE process in the context of CG, CHH and CHG methylation, and theTnt1 retrotransposition correlates with the hyperactive methylation regions. -
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