Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution

Cheng, Rui-Yu; Xie, Deng-Feng; Zhang, Xiang-Yi; Fu, Xiao Wen; He, Xing‐Jin; Zhou, Song‐Dong

doi:10.1155/2022/3909596

Cited by 5 publications

(4 citation statements)

References 144 publications

(150 reference statements)

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“…Disturbance of this rule in P. maritimum and other Amaryllidaceae representatives was found in naturally occurring plants and is not derived by any kind of genetic manipulation. The genetics of the Amaryllidaceae family remain largely unknown [ 44 ]. It has been suggested [ 22 ] that connected stomata occur when two meristemoids are connected.…”

Section: Discussionmentioning

confidence: 99%

Stomata in Close Contact: The Case of Pancratium maritimum L. (Amaryllidaceae)

Saridis

Georgiadou

Shtein³

et al. 2022

Plants

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A special feature found in Amaryllidaceae is that some guard cells of the neighboring stomata form a “connection strand” between their dorsal cell walls. In the present work, this strand was studied in terms of both its composition and its effect on the morphology and function of the stomata in Pancratium maritimum L. leaves. The structure of stomata and their connection strand were studied by light and transmission electron microscopy. FM 4–64 and aniline blue staining and application of tannic acid were performed to detect cell membranes, callose, and pectins, respectively. A plasmolysis experiment was also performed. The composition of the connection strand was analyzed by fluorescence microscopy after immunostaining with several cell-wall-related antibodies, while pectinase treatment was applied to confirm the presence of pectins in the connection strand. To examine the effect of this connection on stomatal function, several morphological characteristics (width, length, size, pore aperture, stomatal distance, and cell size of the intermediate pavement cell) were studied. It is suggested that the connecting strand consists of cell wall material laid through the middle of the intermediate pavement cell adjoining the two stomata. These cell wall strands are mainly comprised of pectins, and crystalline cellulose and extensins were also present. Connected stomata do not open like the single stomata do, indicating that the connection strand could also affect stomatal function. This trait is common to other Amaryllidaceae representatives.

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Section: Discussionmentioning

confidence: 99%

Stomata in Close Contact: The Case of Pancratium maritimum L. (Amaryllidaceae)

Saridis

Georgiadou

Shtein³

et al. 2022

Plants

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“…The preferred codons usually ending with A/U might be determined by the high AT content in the plastomes [65]. Leu was encoded by the most codons; however, the codon preference order was slightly different from that of Allium [66], Ligusticum [67], and most Geraniaceae species [26].…”

Section: Plastome Evolution Of Rorippamentioning

confidence: 95%

Complete Plastomes of Ten Rorippa Species (Brassicaceae): Comparative Analysis and Phylogenetic Relationships

Ren,

Xun,

Jia

et al. 2024

Agronomy

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The genus Rorippa belongs to the family Brassicaceae, and its members usually have high medicinal value. The genus consists of approximately 75 species and mainly grows in the Northern Hemisphere, occurring in every continent except Antarctica. The taxonomy and phylogenetic relationships of Rorippa are still unsettled, largely due to complex morphological variations in Rorippa, which were caused by frequent hybridization events. Here, we sequenced four complete plastid genomes of Rorippa species by Illumina paired-end sequencing. The four new plastid genomes of Rorippa ranged in total size from 154,671 bp for R. palustris to 154,894 bp for R. sylvestris. There are 130 genes in the four plastomes, embodying 8 rRNA, 37 tRNA, and 85 protein-coding genes. Combining with six published plastid genomes, we carried on comparative and phylogenetic analyses. We found that the ten Rorippa plastid genomes were conservative in gene number and order, total size, genomic structure, codon usage, long repeat sequence, and SSR. Fourteen mutational hotspot regions could be selected as candidate DNA barcoding to distinguish Rorippa plants. The phylogenetic trees clearly identified that ten Rorippa species displayed monophyletic relationships within the tribe Cardamineae based on plastomes and nrDNA ITS sequences. However, there are significant cytonuclear discordances in the interspecific relationships within Rorippa, as well as the intergeneric relationships between Rorippa and its related genera. We inferred that the cytonuclear discordance is most likely a result of interspecific hybridization within Rorippa, as well as intergeneric hybridization with its related genera. These plastid genomes can offer precious information for studies of species authentication, evolutionary history, and the phylogeny of Rorippa.

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“…There has been interest in whole plastome data recently (Cheng et al, 2022;Dennehy et al, 2021;Jimenez et al, 2020;Xie et al, 2020). Whole plastome sequence data has been applied to recognize new species and estimate phylogeny in Lycoris (Lou et al, 2022;Zhang et al, 2021;Zhang et al, 2022) without any nuclear sequence data for tree comparison.…”

Section: The Road Aheadmentioning

confidence: 99%

Classification and phylogeny of Amaryllidaceae, the modern synthesis and the road ahead: a review

Meerow

2023

Bol. Soc. Argent. Bot.

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The classification and phylogenetic history of the Amaryllidaceae is reviewed since the dawn of molecular systematics in the 1990’s. The family is now recognized as comprising three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, of which the latter is the largest. The family likely had a Gondwanaland origin in what is now Africa. Agapanthoideae is monotypic, endemic to South Africa, and the first branch in the family tree of life; Allioidieae is sister to Amaryllidoideae. Four tribes are recognized in Allioideae: Allieae (monotypic, with nearly 1000 species of Allium across the Northern Hemisphere), Gilliesieae (5–7 genera in southern South America), Leucocoryneae (six genera mostly in southern South America), and Tulbaghieae (monotypic, with ca. 30 species endemic to South Africa). Amaryllidoideae is cosmopolitan, but mostly pantropical, consisting of 13 tribes. Centers of diversity occur in South Africa, South America and the Mediterranean region. The American clade is sister to the Eurasian clade (tribes Galantheae, Lycorideae, Narcisseae and Pancratieae) of the subfamily. The American Amaryllidoideae resolves as two monophyletic groups, 1) the hippeastroid clade (tribes Griffineae and Hippeastreae) and 2) the Andean tetraploid clade (tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae). Molecular analyses are reviewed for each main clade of the family, along with the resultant taxonomic changes. Directions for future studies are briefly discussed.

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Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution

Cited by 5 publications

References 144 publications

Stomata in Close Contact: The Case of Pancratium maritimum L. (Amaryllidaceae)

Stomata in Close Contact: The Case of Pancratium maritimum L. (Amaryllidaceae)

Complete Plastomes of Ten Rorippa Species (Brassicaceae): Comparative Analysis and Phylogenetic Relationships

Classification and phylogeny of Amaryllidaceae, the modern synthesis and the road ahead: a review

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