The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses

Lu, Ruisen; Li, Pan; Qiu, Ying‐Xiong

doi:10.3389/fpls.2016.02054

Cited by 122 publications

(143 citation statements)

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“…Besides, they found that infA existed but seemed to have lost its function in the Lilium (Liliaceae) cp genome, because it had AAT instead of ATG in the start codon position and includes two premature stop codons. The pseudogenization of infA was also found in Fritillaria (Li et al, 2014) and Cardiocrinum (Lu et al, 2016), close relatives of Lilium . However, our study indicates the loss of infA in Amana .…”

Section: Discussionmentioning

confidence: 77%

“…This is congruent with a typical monocot cp genome structure (Yang et al, 2013). Among other taxa in the family Liliaceae, IR expansion into rps19 has been observed in Lilium (Kim and Kim, 2013), Fritillaria (Li et al, 2014), and Cardiocrinum (Lu et al, 2016). This suggests that the expansion of the IR/LSC junctions into rps19 may be an ancestral symplesiomorphy of the family Liliaceae, and thus provides no relevant phylogenetic information for addressing intrafamilial questions.…”

Section: Discussionmentioning

confidence: 99%

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Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

et al. 2017

Front. Plant Sci.

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The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629–25,859 bp) separated by the large single-copy (81,482–82,218 bp) and small single-copy (17,366–17,465 bp) regions. Each cp genome equivalently contains 112 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 78 protein coding genes. Gene content, gene order, AT content, and IR/SC boundary structure are nearly identical among all Amana cp genomes. However, the relative contraction and expansion of the IR/SC borders among the six Amana cp genomes results in length variation among them. Simple sequence repeat (SSR) analyses of these Amana cp genomes indicate that the richest SSRs are A/T mononucleotides. The number of repeats among the six Amana species varies from 54 (A. anhuiensis) to 69 (Amana kuocangshanica) with palindromic (28–35) and forward repeats (23–30) as the most common types. Phylogenomic analyses based on these complete cp genomes and 74 common protein-coding genes strongly support the monophyly of the genus, and a sister relationship between Amana and Erythronium, rather than a shared common ancestor with Tulipa. Nine DNA markers (rps15–ycf1, accD–psaI, petA–psbJ, rpl32–trnL, atpH–atpI, petD–rpoA, trnS–trnG, psbM–trnD, and ycf4–cemA) with number of variable sites greater than 0.9% were identified, and these may be useful for future population genetic and phylogeographic studies of Amana species.

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Section: Discussionmentioning

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

et al. 2017

Front. Plant Sci.

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“…The intergenic spacer ycf3-trnS has been used in phylogenetic inferences in Asteraceae and Euphorbiaceae (Vilatersana et al 2010;Montes Moreno et al 2010; Barres et al 2011), and the rps3 gene in Poaceae, Verbenaceae and families of Asparagales (Peterson et al 2010;Marx et al 2010;Kim et al 2012). The intergenic spacer ndhE-psaC appears to have not yet been used as a marker for phylogenetic studies, but it was also reported as useful for phylogenetic and phylogeographic studies in Liliaceae (Lu et al 2017). The intergenic spacer ndhC-rbcL is putatively exclusive of Cactaceae, resulting from the trnV-rbcL inversion, and its phylogenetic utility must be further investigated, at least in clades where ndh genes are present.…”

Section: Phylogenetically Informative Regionsmentioning

confidence: 99%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

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“…In the present study, because we conducted field experiments and sampling of material in Hokkaido, we treated the study species as C. cordatum var. glehnii (Lu, Li, & Qui, 2017).…”

Section: Methodsmentioning

confidence: 99%

Inter‐populational variation, but no‐annual variation within populations, in terms of reproductive size and genetic structure in a monocarpic perennial herb, Cardiocrinum cordatum var. glehnii

Hayafune

Utech

Ohara

2018

Plant Species Biology

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Cardiocrinum cordatum var. glehnii (Liliaceae) is a monocarpic perennial herb living in temperate broad‐leaved deciduous forests. In the present study we examined the sizes (basal diameter of the stem and flower numbers) of flowering individuals and genetic diversity using microsatellite loci of 23 populations of C. cordatum var. glehnii in Hokkaido, Japan, over 2 years (2009 and 2010). As a result, we found both the basal stem diameter and the number of flowers varied widely among the populations. However, although the sizes of flowering individuals differed among the populations, these were very stable in each population and in each year. In addition, for genetic diversity, the same trends (i.e. wide variation among the populations but non‐annual variation) were detected.

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The Complete Chloroplast Genomes of Three Cardiocrinum (Liliaceae) Species: Comparative Genomic and Phylogenetic Analyses

Cited by 122 publications

References 61 publications

Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

Comparative Genomics and Phylogenomics of East Asian Tulips (Amana, Liliaceae)

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Inter‐populational variation, but no‐annual variation within populations, in terms of reproductive size and genetic structure in a monocarpic perennial herb, Cardiocrinum cordatum var. glehnii

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