- After the domestication for thousands of years, lotus has differentiated into three cultivated types -flower lotus, seed lotus and rhizome lotus. - homogeneous, whereas the flower lotus was biphyletic and genetically heterogeneous. - Some of the genes in these regions contributed to the essential domestication traits of lotus. - Among cultivated lotus, flower lotus showed the greatest variation. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - Nelumbo Adans., the earliest originating genus among angiosperms, is a surviving living fossil that experienced quaternary glaciation, with an evolutionary history of ap- proximately 135 million years [1, 2]. - Moreover, domestication has modi- fied the distribution of the world’s population. - nucifera have differentiated into three types: rhizome lotus, seed lotus, and flower lotus [21]. - The observed differences in mapping rates were caused by the divergence between the sequenced geno- types and the reference genome of the sacred lotus var- iety ‘China Antique’.. - and average, 0.17%) for rhizome lotus. - Most of the wild sacred lotus accessions showed low heterozy- gosity (Het rate. - The accuracy of the SNPs and the genotyping infer- ences was estimated to be via Polymer- ase Chain Reaction (PCR) and Sanger sequencing (see Additional file 4: Table S4 and Additional file 5: Table S5). - A total of of the detected SNPs were distributed across intergenic regions, and 1.89%. - 1 Morphology of the four lotus groups. - Deletions, insertions, duplication, and inversions accounted for and of the detected SVs(>. - Flower lotus, seed lotus, rhizome lotus, wild sacred lotus, and American lotus differed greatly in terms of the iden- tified SNP numbers. - followed by flower lotus . - seed lotus (8,161,881. - American lotus group possessed the most unique SNPs followed by wild sacred lotus seed lotus flower lotus and rhizome lotus (87,758), which exhibited the fewest SNPs.. - However, rhizome lotus exhibited the few- est number of SNPs. - lutea genome was lowest (1.33), while that for wild sacred lotus was highest (1.47), which was slightly higher than for the cultivated groups (rhizome lotus [1.42], flower lotus [1.41], and seed lotus [1.45]).. - nucifera , flower lotus showed the highest diversity (θπ (10 − 3. - 3.52), followed by seed lotus (θπ (10 − 3. - 2.46), and rhizome lotus ((θπ (10 − 3. - Moreover, wild sacred lotus (θπ (10 − 3. - (rhizome lotus), and the percentage of unique indels was reduced even more sharply, to 2.76% in wild lotus and 0.41% in rhizome lotus. - lutea , followed by flower lotus and wild sacred lotus. - seed lotus dis- played an intermediate number, and rhizome lotus ex- hibited the fewest. - The number of each type of SV and unique SVs in flower lotus was slightly higher than in rhizome lotus. - lotus divergence could begin with splitting tropical- subtropical Eurasian and American species followed by a rise of a common ancestor of the two peripheral temper- ate and Indonesian groups. - nucifera clade, seed lotus accessions and rhizome lotus accessions clustered together, respectively, obviously separating from the wild accessions. - Moreover, flower lotus accessions dis- persed, suggesting their complex genetic background.. - rhizome lotus + 18 wild sacred lotus ac- cessions. - and seed lotus + flower lotus + four wild sacred lotus accessions. - In contrast, seed lotus and flower lotus were more dispersed, indicating higher diver- sity than that of rhizome lotus. - Lotus was first planted in a garden by King Fu Chai in 473 B.C., which marked the beginning of the domestica- tion of flower lotus [30], after which the phenotypes of lotus were gradually differentiated into field lotus and gar- den lotus.. - Based on the NJ tree and PCA results, rhizome lotus shows high genetic differentiation from seed lotus and flower lotus. - Hence, the possibility that rhizome lotus was domesticated independently from different populations of flower lotus and seed lotus was considered. - To further analyze the domestication history of lotus, we constructed a multilevel (K = 2, 3…7) population structure to estimate the maximum likelihood ancestry and the proportion of the ancestral property in each individual (Fig. - Moreover, for K = 2, we found a division between rhizome lotus and seed lotus/flower lotus, and the flower lotus accessions showed evidence of admixture when K = 2, supporting the PCA analysis that flower lotus possibly domesticated from two ancestors. - Meanwhile, a recent history of introgression from wild lotus in flower lotus as identified (K = 4–7).. - Interestingly, a few of the accessions occurred at unex- pected positions in both the PCA diagrams and NJ trees (Fig. - The lower LD found in flower lotus among domesticated groups suggested the occurrence of frequent hybridization events during flower lotus domestication, compared with seed lotus and rhizome lotus. - a The neighbor-joining tree of the 69 lotus accessions with bootstrap =1000 and the bootstrap values less than 100 were labelled. - b Principal component analysis (PCA) of the 69 lotus accessions. - c Population structure (k = 2 – 7) of the 69 lotus accessions determined by FRAPPE. - For rhizome lotus selection, the morphology and yield of the underground stem are the characteristics of inter- est. - In the present study, the combination of F ST (wild lotus/seed lotus, flower lotus/. - wild lotus and rhizome lotus/wild lotus) and θπ analyses was used to detect regions of selection in lotus (Fig. - Seed lotus exhibited the greatest number of se- lected regions and genes, followed by rhizome lotus. - Flower lotus showed the lowest number of selected regions and genes. - Data points located to the right of the right vertical dashed lines (corresponding to the 5% right tails of the log_2 π ratio distribution, where the log2 π ratio is 2.27 in (a), 0.46 in (b), 3.87 in (c)) and above the horizontal dashed line (the 5% right tail of the Z(F ST ) distribution, where Z(F ST ) is 1.21 in (a), 1.82 in (b), 2.22 in (c)) were identified as selected regions for seed lotus, flower lotus and rhizome lotus(blue points), respectively. - The resistance genes identified among the selected genes provide clas- sical evidence of flower lotus domestication. - For ex- ample, one of the selected genes encodes 3-oxo-Δ 4,5- steroid 5β-reductase (XM which is a key enzyme in the synthesis of cardiac glycoside [40](Fig. - insects and mammals, thus enhancing insect resistance in flower lotus. - and may inhibit flowering in rhizome lotus as well (Fig. - In the first column of the graph, the pi-1 and pi-2 stand for the pi values of the selected genes of flower lotus and wild lotus respectively. - the pi-1 and pi-2 stand for the pi values of rhizome lotus and wild lotus respectively in the second column and the pi-1 and pi-2 stand for the pi values of wild lotus and seed lotus respectively in the third column. - Therefore, this selected gene improves the size of rhizome lotus.. - For example, in the early Western Zhou Dynasty (1046 B.C.―771 B.C), lotus rhizome was one of the 40 vegeta- bles recorded in China, which means that rhizome lotus domestication occurred 3000 years ago [28]. - Although domestication has ob- viously significantly increased the heterozygosity and the level of genetic diversity in lotus cultivars compared to the wild lotus, among the three cultivated groups, flower lotus exhibited the greatest variation, followed by seed lotus and rhizome lotus showed the lowest variation. - People prefer cross-breeding of flower lotus and seed lotus, rather than rhizome lotus. - On the other hand, according to archaeological discoveries and history records domestication of three types of cultivated lotus began in the middle and down- stream of the Yellow River and Yangtze River [50], which is a small area compared with the distribution area of the lotus. - Thus, the low motivation for lotus breeding espe- cially in rhizome lotus and the relatively narrow origin of cultivated lotus may negatively influence the sustainable development of the lotus industry. - A total of 74.99% of the detected SNPs were distributed across intergenic re- gions, and 1.89% of the detected SNPs were distrib- uted across CDSs. - Flower lotus showed the greatest variation, followed by seed lotus and then rhi- zome lotus. - Table 2 Statistics of the regions under selection in lotus groups. - Seed lotus . - Rhizome lotus. - The insert size of the libraries was 500 bp, and the paired-end reads were 125 bp. - as the reference genome (ftp://ftp.ncbi.nlm.nih.gov/ge- nomes/all/GCA Chinese_Lotus_1.1), and BWA (0.7.10) software [52] was used to map all the reads from each sample to the reference genome. - Het- erozygosity was the quotient of the number of heterozy- gous SNPs divided by total chromosome length. - After add- ing headers for processing of the reads, realignment around indels was performed with the Realigner TargetCreator package to identify regions that needed to be realigned. - Geographic distribution of the 69 lotus accessions. - pink, flower lotus. - green, seed lotus. - blue, rhizome lotus). - Venn diagrams of the unique and common single-nucleotide polymorphisms (SNPs) in the five groups. - Venn diagrams of the unique and common short insertion and deletions (indels) in the five groups. - Analysis of the phylogenetic relationships and population structure of wild sacred lotus. - Morphology of the three lotus accessions based on multiple traits. - Flower lotus accession F05 (D) exhibits both attractive flowers and swollen rhizomes. - Gene Ontology analysis of the genes under artificial selection in seed lotus.. - Kyoto Encyclopedia of Genes and Genomes analysis of the genes under artificial selection in seed lotus.. - Gene Ontology analysis of the genes under artificial selection in flower lotus.. - Kyoto Encyclopedia of Genes and Genomes analysis of the genes under artificial selection in flower lotus.. - Gene Ontology analysis of the genes under artificial selection in rhizome lotus.. - Kyoto Encyclopedia of Genes and Genomes analysis of the genes under artificial selection in rhizome lotus.. - The lists of the genes at 1% level as signals under artificial selection in cultivated lotus groups.. - Classification and distribution of the genus Nelumbo Adans.. - Purity of the sacred lotus, or escape from contamination in biological surfaces. - Analysis of the connotations and the evolution of the ancient culture of lotus [J]. - Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops. - Genome of the long-living sacred lotus ( Nelumbo nucifera Gaertn). - Preliminary study of the eco-types of genetic resources of tropical Lotus [J]. - Analysis of the nutritional composition of Chinese main lotus seed varieties. - Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts agrobacterium-mediated transformation. - Characterization and expression analysis of the expansin gene NnEXPA1 in lotus Nelumbo nucifera. - An overview of the origin of lotus cultivation in ancient China
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