Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms

Saada, Omar Abou; Friedrich, Anne; Schacherer, Joseph

doi:10.1016/j.ygeno.2022.110369

Cited by 7 publications

(4 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, the built-in heuristic algorithms of multiple reference-based or de novo phasing tools have been systematically summarized [34] , [59] , [60] . However, many have been developed for the human genome and have not been applied well to plant genome assembly.…”

Section: Toward Haplotype-resolved Assemblymentioning

confidence: 99%

“…In reference-based variant phasing, a high-quality genome is required as the reference to distinguish different haplotypes based on long-range linked allelic variants through alignments of sequencing reads against the reference genome using different phasing algorithms, including minimum error correction [91] , weighted minimum letter flip [59] , maximum fragment cut [92] , and polyploid balanced optimal partition [93] as different frameworks [34] , [59] , [60] . More than 20 reference-based variant phasing tools have been developed ( Table S1 ).…”

Section: Toward Haplotype-resolved Assemblymentioning

confidence: 99%

See 1 more Smart Citation

Recent Advances in Assembly of Complex Plant Genomes

Kong¹,

Wang²,

Zhang³

et al. 2023

Genomics, Proteomics &Amp; Bioinformatics

View full text Add to dashboard Cite

Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.

show abstract

Section: Toward Haplotype-resolved Assemblymentioning

confidence: 99%

Section: Toward Haplotype-resolved Assemblymentioning

confidence: 99%

Recent Advances in Assembly of Complex Plant Genomes

Kong¹,

Wang²,

Zhang³

et al. 2023

Genomics, Proteomics &Amp; Bioinformatics

View full text Add to dashboard Cite

show abstract

“…Another difficulty in accurate assembly of allopolyploid genomes has been ‘phasing’ i.e., the assignment of assembly contigs to the correct subgenome. Switch errors and misassemblies introduced during the assembly process can impair the signals required to successfully phase a scaffold, and potential crossover interactions between homoeologs can further complicate this signal [ 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Winter,

Taranto,

Yimer

et al. 2024

PLoS ONE

View full text Add to dashboard Cite

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.

show abstract

“…Another difficulty in accurate assembly of allopolyploid genomes has been ‘phasing’ ie, the assignment of assembly contigs to the correct subgenome. Switch errors and misassemblies introduced during the assembly process can impair the signals required to successfully phase a scaffold, and potential crossover interactions between homoeologs can further complicate this signal [8,9] .…”

Section: Introductionmentioning

confidence: 99%

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Winter

Taranto

Yimer

et al. 2023

Preprint

View full text Add to dashboard Cite

We present the chromosome-scale genome of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly is annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes are phased using ancestral k-mer spectral analysis. Subgenome B appears to show greater fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identify regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. Indels are common both between alleles within a subgenome, and between the A and B subgenomes, suggesting the M. javanica genome exists in a dynamic hypo-tetraploidy where copy number can vary along the chromosome. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.

show abstract

Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms

Cited by 7 publications

References 38 publications

Recent Advances in Assembly of Complex Plant Genomes

Recent Advances in Assembly of Complex Plant Genomes

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

Contact Info

Product

Resources

About