The Asian lotus (&lt;i&gt;Nelumbo nucifera&lt;/i&gt;) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

Liao, Xuezhu; Gu, Cuihua; Xiang, Kunli; Wang, Jie; Li, Sen; Tembrock, Luke R.; Wu, Zhiqiang; He, Wenchuang

doi:10.48130/opr-2022-0002

Cited by 9 publications

(8 citation statements)

References 56 publications

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“…Previous studies have reported that plastomes within a species are highly conserved in terms of genomic structure, GC content, gene content, and the synteny of gene order [ 26 , 28 ], with D. alata being no exception in this regard. The pan-plastome of D. alata constructed here indicated that all 52 accessions (153,114–153,161 bp) from different geographical areas possessed the typical quadripartite structure of land plant plastomes, with a pair of IR regions (25,464 bp) separating the LSC (83,351–83,415 bp) and SSC (18,815–18,836 bp) regions, and encoded the same 113 unique genes, including 79 PCGs, 30 tRNAs, and 4 rRNAs ( Figure 1 , Table S1 ).…”

Section: Discussionmentioning

confidence: 99%

“…Due to the absence of recombination, low levels of nucleotide substitution, uniparental mode of inheritance, and small effective population size [ 20 , 21 ], plastome sequences have been widely used for accurate species identification and phylogenetic inference in different plant lineages [ 21 , 22 , 23 ]. More recently, pan-plastomes have been developed to capture inter- and intraspecific variations [ 24 , 25 , 26 ]. For example, Magdy et al [ 25 ] constructed high-resolution pan-plastomes from 321 Capsicum accessions to differentiate cultivars and lineages.…”

Section: Introductionmentioning

confidence: 99%

“…For example, Magdy et al [ 25 ] constructed high-resolution pan-plastomes from 321 Capsicum accessions to differentiate cultivars and lineages. Wang et al [ 26 ] de novo assembled the plastomes of 316 Nelumbo accessions to construct a reliable pan-plastome map and investigate the phylogeography and genetic diversity among them. Furthermore, these studies also indicated that pan-plastomes have several advantages over nuclear pan-genomes, such as (i) easier assembly that is not affected by polyploids, (ii) much more complete reference sequences for assembly, annotation, and comparison, and (iii) the absence of large duplicate syntenic regions, thus relieving the effects of gene paralogy in molecular systematics [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

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Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Zhang

et al. 2023

IJMS

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“…For example, Magdy et al [ 30 ] used a pan-plastome developed from 321 complete plastomes to evaluate the genetic variation of cultivated Capsicum species leading to an improved classification system between the different cultivars. Wang et al [ 31 ] constructed a pan-plastome using 316 lotus ( Nelumbo sp.) accessions to investigate the phylogeographic and genetic diversity of the only two extant species in this living fossil lineage.…”

Section: Introductionmentioning

confidence: 99%

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

Wang

Liao

et al. 2023

BMC Plant Biol

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Background Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. Results In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. Conclusions The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.

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“…The conserved structure, high copy number within a cell, small size (ca. 110–180 Kb), and uniparental inheritance, have made plastomes an ideal source of data for phylogenetic reconstruction (Li et al, 2021), population genomics (He et al, 2021; Wang et al, 2022), and species delimitation (Leliaert et al, 2014). Despite the highly conserved nature of plastomes, variation in plastome structure, size, gene content, and collinearity can be found across most tracheophytes (Palmer & Stein, 1986; Odintsova & Yurina, 2006; Ruhlman & Jansen, 2014).…”

Section: Introductionmentioning

confidence: 99%

Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae

Wang

Tembrock

et al. 2022

J of Sytematics Evolution

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The study of genomic structural evolution associated with accelerated evolutionary rates that result in avoidance of meltdown and increase biodiversity is becoming ever more possible as the number of available plastomes increases. To more comprehensively analyze rate heterogeneity among monocots and within Poaceae, we sequenced plastomes from four Poaceae species, combined them with publicly available data from ~200 plastomes, and conducted comparative analyses to quantify the pattern of rate heterogeneity between different lineages, functional groups, and periods of evolutionary time. We compared structural differences across the Poaceae to quantify how changes in plastome size correspond to different genomic subunits and the evolution of IR-SC junction boundaries. The substitution rates among ancestral Poaceae were inferred to be exceptionally rapid compared to other monocots but slowed after divergence into extant lineages, which could not be sufficiently explained by positive selection. As such, rapid rates in the ancestral lineage leading to Poaceae might be more closely linked to large-scale structural changes like the loss of ycf1 and ycf2. The total increase in plastome size across Poaceae was positively correlated with the total length of intergenic spacers, tandem repeats, and dispersed repeats as well as large single copy, and inverted repeats (IRs). The continuous evolution of IR-SC junction boundaries was asynchronous with sizes of total genome and subunits across Poaceae. Future work is needed to better understand what factors in ancestral Poaceae evolved to harness such rapid rates of plastome evolution, avoid a mutational meltdown, and escape the stagnation of strong purifying selection as well as if these factors could be utilized to synthetically control rates.

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The Asian lotus (<i>Nelumbo nucifera</i>) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

Cited by 9 publications

References 56 publications

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses

The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae

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