Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP)

Bog, Manuela; Lautenschlager, Ulrich; Landrock, Maria F.; Landolt, Elias; Fuchs, Joerg; Sree, K. Sowjanya; Oberprieler, Christoph; Appenroth, Klaus‐J.

doi:10.1007/s10750-014-2163-3

Cited by 41 publications

(45 citation statements)

References 33 publications

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“…The resulting v.2 assembly (Sp9509v2) with new joins validated by gDNA PCR had 23 super‐scaffolds of more than 1 Mb each, and an N50 length of 5.8 Mb (Figure b; Table S1). Sp9509v2 approaches the expected 20 chromosomes of the 1 n genome of Spirodela (Wang et al ., ; Bog et al ., ).…”

Section: Resultsmentioning

confidence: 97%

“…They are some of the fastest growing angiosperms in the world, and their aquatic habitat and small size make their cultivation and harvesting at large scales relatively straightforward. The Greater Duckweed, Spirodela polyrhiza, has the smallest genome of the duckweed family at 158 Mb (Wang et al, 2011;Bog et al, 2015) and propagates asexually through budding from its reduced leaf-stem (frond) structure ( Figure 1a). To unleash the great potential of duckweed as a new model plant as well as facilitating its domestication into a sustainable new crop using molecular breeding approaches, a reference genome of high resolution and fidelity would be essential.…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

et al. 2017

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Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.

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Section: Resultsmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

et al. 2017

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“…Consequently, S. polyrhiza often achieves extremely high census population sizes in nature as millions of individuals can be found in a single pond. However, previous studies using a limited number of genetic markers found low genetic diversity ( 11, 12 ).…”

Section: Main Textmentioning

confidence: 88%

Low genetic variation is associated with low mutation rate in the giant duckweed

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et al. 2018

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One Sentence Summary: The low-down on a tiny plant: extremely low genetic diversity in an 34 aquatic plant is associated with its exceptionally low mutation rate. 35 36 Main Text 37Explaining within-species genetic diversity-measured as the level of intraspecific DNA 38 sequence variation-is a major goal in evolutionary and conservation biology, as this diversity 39 can influence how species cope with changing environments (1, 2). While intraspecific genetic 40 diversity is known to vary widely among species, the underlying causes remain controversial (3, 41 4). According to population genetic theory, the population mutation parameter (q ) is determined 42 by the product of the spontaneous neutral mutation rate (µ) and effective population size (Ne), 43 and in diploid species q = 4 ´ Ne ´ µ (5). In practice, the parameter q is often estimated by the 44 average pairwise nucleotide diversity (p) at putatively neutral sites (6). While the role of Ne in 45 explaining variation in genetic diversity among taxa has received much theoretical and empirical 46 attention (3, 4, 7), the influence of variation in mutation rate and the interaction between Ne and 47

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“…The genomes of S. polyrhiza clones 7498 (Wang et al, 2014) and 9509 (Michael et al, 2017) have been sequenced because of this species' ancestral position among duckweeds and its small genome size (Wang et al, 2011;Bog et al, 2015). By means of mcFISH, 96 anchored and fingerprinted BACs, representing 32 pseudomolecules assembled from genome sequences of clone 7498 using a combination of short-read and BACend sequencing approaches, were integrated into its 20 chromosome pairs (Cao et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies

et al. 2018

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Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules, and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes (BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual chromosome models. We validated both maps further to resolve these differences and addressed whether they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome models. We found no major structural rearrangements between these seven clones, identified seven chimeric pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza genome map with high contiguity was produced with the ON sequence data and genome-wide synteny analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the complementarity of independent approaches to produce whole-genome assemblies in the absence of a genetic map.

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Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP)

Cited by 41 publications

References 33 publications

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

Comprehensive definition of genome features in Spirodela polyrhiza by high‐depth physical mapping and short‐read DNA sequencing strategies

Low genetic variation is associated with low mutation rate in the giant duckweed

Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies

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