Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca

Yi, Liuxi; Sa, Rula; Shu-wen, Zhao; Zhang, Xiaoming; Lü, Xudong; Mu, Yingnan; Bateer, Siqin; Su, Shaofeng; Wang, Shuyan; Li, Zhiwei; Shi, She‐Po; Zhao, Xiaoqing; Lu, Zhanyuan

doi:10.3389/fgene.2022.884081

Cited by 8 publications

(7 citation statements)

References 56 publications

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“…Here, to explore effectual phased tools and strategies for assembling complex plant genomes, we have summarized the recently published haplotype-resolved assemblies in plant genomes. We have further divided these assembly approaches into two strategies: reference-based variant phasing and de novo assembly-based haplotype phasing ( Table 1 ) [12] , [51] , [14] , [15] , [16] , [17] , [18] , [61] , [62] , [63] , [64] , [65] , [66] , [67] , [68] , [69] , [70] , [71] , [72] , [73] , [74] , [75] , [76] , [77] , [78] , [79] , [80] , [81] , [82] , [83] , [84] , [85] , [86] , [87] , [88] , [89] , [90] .…”

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

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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.

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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

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“…oleracea [ 10 ], A. cruentus [ 56 ], Su. glauca [ 96 ], Haloxylon ammodendron [ 87 ], P. amilis [ 31 ], D. caryophyllus [ 100 ], G. paniculata [ 51 ], and Bougainvillea .…”

Section: Methodsmentioning

confidence: 99%

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

Lan

Zhao

et al. 2023

Horticulture Research

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Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract colouration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana ‘Mrs. Butt’, a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151,756,278 bp and contains 86,572 genes which undergone a recent WGD. We confirmed that multiple rounds of whole genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colours in Bougainvillea, we analyzed the genes involved in betalains and anthocyanins biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with the bract colour, and the higher expression level in the betalain biosynthetic pathway is required for the coloured bract. The improved understanding of the correlation between gene expression and bract colour allows plant breeding outcomes to be predicted with greater certainty.

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“…Interestingly, almost half of the DEGs involved in the phenylpropanoid biosynthesis pathway were found to be peroxidase, which was consistent with the germination response of Indian mustard exposed to drought stress ( Wei et al., 2023 ). Interestingly, except for peroxidase 3 ( SgPER3 ), almost all DEGs encoding peroxidase were obtained in the genome of S. glauca ( Yi et al., 2022 ). Singh et al.…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

Wang,

Xu,

et al. 2024

Front. Plant Sci.

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Suaeda glauca Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA3 effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA3 on S. glauca black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA3 treatment were analyzed and compared, and the TTF, H2O2, O2–, starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA3 treatment significantly increased seed vigor, H2O2, and O2– contents but decreased starch and soluble sugar contents of S. glauca black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (SgGA3ox1, SgKAO and SgGA2ox8) and ABA signal transduction (SgPP2Cs) could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA3 treatment conditions, especially many SgPER genes encoding peroxidase. In addition, exogenous GA3 treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA3-induced dormancy release, such as SgBAM, SgHXK2, and SgAGLU, etc. In a word, exogenous GA3 effectively increased the germination rate and seed vigor of S. glauca black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA3 on the dormancy release of S. glauca black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.

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Chromosome-Scale, Haplotype-Resolved Genome Assembly of Suaeda Glauca

Cited by 8 publications

References 56 publications

Recent Advances in Assembly of Complex Plant Genomes

Recent Advances in Assembly of Complex Plant Genomes

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

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