<i>De novo</i> phasing resolves haplotype sequences in complex plant genomes

Guk, Ji‐Yoon; Jang, Min-Jeong; Choi, Jinwook; Lee, Yeon Mi; Kim, Seungill

doi:10.1111/pbi.13815

Cited by 15 publications

(8 citation statements)

References 48 publications

(88 reference statements)

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“…The majority of the genes were found to be in a collinear arrangement, where those genes and the order of the genes were conserved between the two haplotypes. Size variations and copy number variations between haplotypes have been extensively reported in other studies (Guk et al 2022).…”

Section: Discussionmentioning

confidence: 65%

The Genomes of Australian Wild Limes

Nakandala,

Furtado,

Masouleh

et al. 2024

Preprint

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Australian wild limes occur in highly diverse range of environments and are a unique genetic resource within the genus Citrus. Here we compare the haplotype-resolved genome assemblies of six Australian native limes, including four new assemblies generated using PacBio HiFi and Hi-C sequencing data. The size of the genomes was between 315 and 391 Mb with contig N50s from 29.5 to 35 Mb. Gene completeness of the assemblies was estimated to be from 98.4–99.3% and the annotations from 97.7–98.9% based upon BUSCO, confirming the high contiguity and completeness of the assembled genomes. High collinearity was observed among the genomes and the two haplotype assemblies for each species. Gene duplication and evolutionary analysis demonstrated that the Australian citrus have undergone only one ancient whole-genome triplication event during evolution. The highest number of species-specific and expanded gene families were found in C. glauca and they were primarily enriched in purine, thiamine metabolism, amino acids and aromatic amino acids metabolism which might help C. glauca to mitigate drought, salinity, and pathogen attacks in the drier environments in which this species is found. Unique genes related to terpene biosynthesis, glutathione metabolism, and toll-like receptors in C. australasica, and starch and sucrose metabolism genes in both C. australis and C. australasica might be important candidate genes for HLB tolerance in these species. Expanded gene families were not lineage specific, however, a greater number of genes related to plant-pathogen interactions, predominantly disease resistant protein, was found in C. australasica and C. australis.

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Section: Discussionmentioning

confidence: 65%

The Genomes of Australian Wild Limes

Nakandala,

Furtado,

Masouleh

et al. 2024

Preprint

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“…The sequencing of plant genomes has greatly advanced our understanding of plant development, evolution, and the formation of biological traits (Hamilton & Robin Buell, 2012). De novo assembly of highly heterozygous genomes can yield haplotype genomes, providing additional insights into structural variations (SVs) and allele‐specific expression (ASE) between haplotypes (Guk et al., 2022). ASE is considered to play a significant role in genetics by contributing to heterosis, and the dominant effect and overdominant effect have been proposed to explain the genetic basis of heterosis (Liu et al., 2020; Shao et al., 2019).…”

Section: Introductionmentioning

confidence: 99%

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

Lu,

Chen,

et al. 2024

The Plant Journal

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SUMMARYPhanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high‐coverage PacBio and Hi‐C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes: Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole‐genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele‐specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high‐quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.

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“…For highly heterozygous species, a haplotype-resolved genome could be combined with a T2T genome assembly to construct a superior reference genome (i.e. haplotype-resolved T2T genome) [ 10 ]. The first chromosome-level genome assemblies were generated in Mentha longifolia ( M. longifolia ) (2n = 2x = 24) [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens ‘Variegata’

Yang,

Wang,

Zhou

et al. 2024

Horticulture Research

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Mentha is a commonly used spice worldwide, which possesses medicinal properties and fragrance. These characteristics are conferred, at least partially, by essential oils such as menthol. In this study, a gap-free assembly with a genome size of 414.3 Mb and 31,251 coding genes was obtained for Mentha suaveolens ‘Variegata’. Based on its high heterozygosity (1.5%), two complete haplotypic assemblies were resolved, with genome sizes of 401.9 Mb and 405.7 Mb, respectively. The telomeres and centromeres of each haplotype were almost fully annotated. In addition, we detected a total of 41,135 structural variations. Enrichment analysis demonstrated that genes involved in terpenoid biosynthesis were affected by these structural variations. Analysis of volatile metabolites showed that Mentha suaveolens mainly produces piperitenone oxide rather than menthol. We identified three genes in the Mentha suaveolens genome which encode isopiperitenone reductase (ISPR), a key rate-limiting enzyme in menthol biosynthesis. However, the transcription levels of ISPR were low. Given that other terpenoid biosynthesis genes were expressed, Mentha suaveolens ISPRs may account for the accumulation of piperitenone oxide in this species. The findings of this study may provide a valuable resource for improving the detection rate and accuracy of genetic variants, thereby enhancing our understanding of their impact on gene function and expression. Moreover, our haplotype-resolved gap-free genome assembly offers novel insights into molecular marker-assisted breeding of Mentha.

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De novo phasing resolves haplotype sequences in complex plant genomes

Cited by 15 publications

References 48 publications

The Genomes of Australian Wild Limes

The Genomes of Australian Wild Limes

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

A haplotype-resolved gap-free genome assembly provides novel insight into monoterpenoid diversification in Mentha suaveolens ‘Variegata’

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