Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (<i>Nelumbo nucifera</i>)

Huang, Longyu; Yang, Mei; Li, Ling; Li, Hui; Yang, Dong; Shi, Tao; Yang, Pingfang

doi:10.1111/jipb.12606

Cited by 44 publications

(55 citation statements)

References 62 publications

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“…Based on continuous phenotype measurement results of 390 lotus germplasms from 2013 to 2015, 10 LA and 10 SA lotus germplasms were selected from 43 representatives showing extreme plant architecture phenotypes, and WGRS was performed to detect genome-wide DNA polymorphisms among the 20 selected lotus germplasms. The average sequencing depth of the 20 high-quality datasets reached 12.22×, which was much deeper than the average sequencing depth of 4× reported in previous GWRS studies in the lotus ( Huang et al, 2018 ). The deep sequencing depth ensured a high level of confidence in the detected DNA polymorphisms.…”

Section: Discussioncontrasting

confidence: 51%

“…The genome sequences of two lotus individuals have been released ( Ming et al, 2013 ; Wang et al, 2013 ), enabling WGRS in the lotus. At present, WGRS has only been applied in evolutionary studies on 19 lotus germplasms and in detecting genome-wide simple sequence repeat (SSR) markers by WGRS in ‘Chiang Mai wild lotus’ ( Hu et al, 2015 ; Huang et al, 2018 ). However, few trait-associated variants have been identified in the lotus.…”

Section: Introductionmentioning

confidence: 99%

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Detection of Highly Differentiated Genomic Regions Between Lotus (Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture

et al. 2018

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The lotus (Nelumbo nucifera Gaertn.) is one of the most economically and ornamentally important perennial aquatic plants. Plant architecture is an important trait for lotus classification, cultivation, breeding, and applications. In this study, traits representing plant architecture were measured in 390 lotus germplasms for 3 years. According to the phenotypic distribution, 21 large architecture (LA) and 22 small architecture (SA) germplasms exhibiting extreme phenotypes were selected as representatives of plant architecture. Microscopy analyses revealed that LA lotuses possessed far more vertical cells and longer cell lengths than SA lotuses, and there was a closer linear relationship between vertical cell number and plant architecture than cell length and plant architecture. Furthermore, based on whole genome re-sequencing data from 10 LA and 10 SA lotus germplasms, fixation index (FST) genome scan identified 11.02 Mb of genomic regions that were highly differentiated between the LA and SA lotus groups. Chi-square test revealed that 17,154 single nucleotide polymorphisms (SNPs) and 1,554 insertions and deletions (InDels) showed distinct allelic distribution between the LA and SA lotus groups within these regions. A total of 126 variants with distinct allelic distribution in the highly differentiated region were predicted to cause amino acid changes in 60 genes. Among the 41 genes with functional annotation, the expression patterns of six genes involved in cell division and cell wall construction were confirmed using quantitative reverse-transcription PCR (qRT-PCR). In addition, 34 plant architecture-associated InDel markers were developed and verified in the remaining 11 LA and 12 SA lotus plant architecture representatives. This study identified promising functional markers and candidates for molecular breeding and will facilitate further elucidation of the genetic mechanisms underlying plant architecture in the lotus.

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Section: Discussioncontrasting

confidence: 51%

Section: Introductionmentioning

confidence: 99%

Detection of Highly Differentiated Genomic Regions Between Lotus (Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture

et al. 2018

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“…Illumina resequencing data from 18 Asian lotus individuals including rhizome lotus, flower lotus, seed lotus, wild lotus, and Thai lotus were downloaded from NCBI ( supplementary data , Supplementary Material online) ( Huang et al. 2018 ).…”

Section: Methodsmentioning

confidence: 99%

Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

Shi

Rahmani

Gugger

et al. 2020

Molecular Biology and Evolution

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For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant.

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“…Genome sequences of lotus have been published, laying a foundation for the analysis of genome variation [21,22]. Up to date, few accessions were used to analysis the whole-genome variation of lotus [23]. Knowledge of genetic divergence and selection of their genomes during its domestication remains limited.…”

Section: Introductionmentioning

confidence: 99%

Comparative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera

Zhu

Zheng

et al. 2020

BMC Genomics

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Background: Lotus (Nelumbo nucifera) is an aquatic plant with important agronomic, horticulture, art and religion values. It was the basal eudicot species occupying a critical phylogenetic position in flowering plants. After the domestication for thousands of years, lotus has differentiated into three cultivated types-flower lotus, seed lotus and rhizome lotus. Although the phenotypic and genetic differentiations based on molecular markers have been reported, the variation on whole-genome level among the different lotus types is still ambiguous. Results: In order to reveal the evolution and domestication characteristics of lotus, a total of 69 lotus accessions were selected, including 45 cultivated accessions, 22 wild sacred lotus accessions, and 2 wild American lotus accessions. With Illumina technology, the genomes of these lotus accessions were resequenced to > 13× raw data coverage. On the basis of these genomic data, 25 million single-nucleotide polymorphisms (SNPs) were identified in lotus. Population analysis showed that the rhizome and seed lotus were monophyletic and genetically homogeneous, whereas the flower lotus was biphyletic and genetically heterogeneous. Using population SNP data, we identified 1214 selected regions in seed lotus, 95 in rhizome lotus, and 37 in flower lotus. Some of the genes in these regions contributed to the essential domestication traits of lotus. The selected genes of seed lotus mainly affected lotus seed weight, size and nutritional quality. While the selected genes were responsible for insect resistance, antibacterial immunity and freezing and heat stress resistance in flower lotus, and improved the size of rhizome in rhizome lotus, respectively. Conclusions: The genome differentiation and a set of domestication genes were identified from three types of cultivated lotus-flower lotus, seed lotus and rhizome lotus, respectively. Among cultivated lotus, flower lotus showed the greatest variation. The domestication genes may show agronomic importance via enhancing insect resistance, improving seed weight and size, or regulating lotus rhizome size. The domestication history of lotus enhances our knowledge of perennial aquatic crop evolution, and the obtained dataset provides a basis for future genomics-enabled breeding.

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Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

Cited by 44 publications

References 62 publications

Detection of Highly Differentiated Genomic Regions Between Lotus (Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture

Detection of Highly Differentiated Genomic Regions Between Lotus (Nelumbo nucifera Gaertn.) With Contrasting Plant Architecture and Their Functional Relevance to Plant Architecture

Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants

Comparative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera

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