Assembly of complete diploid phased chromosomes from draft genome sequences

Minio, Andrea; Cochetel, Noé; Vondras, Amanda M.; Massonnet, Mélanie

doi:10.1101/2021.11.11.468134

Cited by 6 publications

(6 citation statements)

References 80 publications

(126 reference statements)

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“…Several approaches have been used to try and correct haplotype switching and produce an accurate fully phased genome. Prior to HiFi reads, haplotype phasing was often highly involved and relied on single nucleotide polymorphism (SNP) data or germ cell sequencing (Minio et al, 2017;Shi et al, 2019;Campoy et al, 2020;Minio et al, 2022). Falcon and Falcon-Unzip assemblers corrected the high error rate of PacBio Continuous Long Read Sequencing (CLR) and used differences in SNPs to partition haplotypes (Chin et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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Section: Discussionmentioning

confidence: 99%

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

2024

Frontiers Research Topics

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“…Trio binning approach differs from the applied for assemblies of other grapevine cultivars generated as pseudo-haplotypes, which exhibit inflated primary assemblies compared to the haplotigs 6,9,11–14,42 . Nonetheless, recently developed bioinformatic tools help to improve the proper assignment of primary contigs to the two haplophases in those cases 16 .…”

Section: Discussionmentioning

confidence: 99%

“…In addition to the PN40024 reference genomes, several additional cultivars have seen their genomes assembled from Pacific Biosciences (PacBio) long reads using the haplotype-aware assemblers FALCON-unzip 6,9,11–14 . FALCON-unzip outputs pseudo-haplotypes, which usually represent a single allele at each position without preserving phase information across the genome 15 , although tools such as HaploSync have been developed to completely phase this type of assemblies 16 . In this context, the combination of multiple sequencing technologies such as Oxford Nanopore Technologies (ONT) and short reads 21 , the use of PacBio HiFi and newer algorithms such as HiFiasm 17 , as well as information from parent-offspring trios 15 have notably improved assembly phasing and quality of grapevine genomes 4,18 19 .…”

Section: Introductionmentioning

confidence: 99%

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

Calderón,

Carbonell-Bejerano,

Muñoz

et al. 2023

Preprint

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Grapevine cultivars (Vitis viniferaL. ssp.vinifera) must be clonally propagated because of their highly heterozygous genomes. Malbec, a France-originated cultivar appreciated for the production of high-quality wines, is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly andab initioprediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes in the Magdeleine-inherited haplotype, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, leading to overexpression of secondary metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation.

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“…BRAKER was used in default mode for RNASeq data, with an additional option for softmasked reference assemblies (--softmasking). Finally, we excluded (as possible pseudogenes) any genes with exons that overlapped annotated repeats and filtered for specific criterion related to gene integrity (Minio et al ., 2021).…”

Section: Methodsmentioning

confidence: 99%

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

Solares

Morales‐Cruz

Figueroa‐Balderas

et al. 2022

Preprint

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Many economically important crops lack suitable genomic tools and annotations, including avocado (Persea americana). We created a reference genome from the Gwen varietal, which is closely related to the agronomically dominant Hass varietal. We produced a 1,032Mb genome assembly with an N50 of 3.37Mb, and a BUSCO score of 91%. We scaffolded the assembly using a genetic map, which led to 12 pseudo-chromosomes representing 78% of the expected genome size containing 49,450 genes. To investigate the domestication history of avocado, we also compiled a database of 34 resequenced genomes that represented major cultivars and the three botanical races of P. americana. Also, in order to elucidate the heterodichomagous nature of avocados, we took into consideration an even distribution of both flowering types in our selection of accessions. Our analyses were consistent with a separate domestication event for each race, and we estimated early genetic separation, with the Mexican race diverging from the Lowland (formerly known as 'West Indian') and Guatemalan races >1 million years ago. We identified putative targets of selective sweeps within domestication; within the Guatemalan race, putative candidate genes were enriched for fruit development and ripening, while the Lowland and Mexican races shared more putative domestication genes than expected at random. We also investigated divergence between races and especially between heterodichomagous flower types. The latter identified genes enriched for functions in pollination, flower development, circadian rhythm and photoperiodism. Genes in regions of divergence were also enriched for GO functions in pollination and flower development.

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Assembly of complete diploid phased chromosomes from draft genome sequences

Cited by 6 publications

References 80 publications

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

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