Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae)

Pacheco, Túlio Gomes; Silva, Gleyson Morais da; Lopes, Amanda de Santana; Oliveira, José Daniel de; Rogalski, Juliana Marcia; Balsanelli, Eduardo; Souza, Emanuel Maltempi de; Pedrosa, Fábio de Oliveira; Rogalski, Marcelo

doi:10.1007/s00425-020-03427-w

Cited by 10 publications

(7 citation statements)

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“…Here, we detected 230 SSRs in the plastome of P. cirrhiflora, most of them being mono-and dinucleotides composed by A and T, occurring mainly in intergenic spacers (Table 3 and Supplementary Table S2). This pattern was also observed in Passiflora edulis (Cauz-Santos et al 2017) and other studies analyzing other angiosperm lineages (Wheeler et al 2014;George et al 2015;Lopes et al 2018c;Pacheco et al 2020b).…”

Section: Events Of Ir Expansion and Contraction Among Speciessupporting

confidence: 84%

“…Most RNA editing sites predicted here change amino acids from polar to nonpolar, which increases the protein hydrophobicity affecting its structural feature and transmembrane domains (He et al 2016). This tendency is also reported in several other studies (He et al 2016;Lopes et al 2018aLopes et al , 2019Pacheco et al 2020b).…”

Section: Events Of Ir Expansion and Contraction Among Speciessupporting

confidence: 79%

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The complete plastome of Passiflora cirrhiflora A. Juss.: structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides

et al. 2020

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The family Passifloraceae contains approximately 1000 species distributed in 36 genera. Passiflora, a species-rich genus, is divided into five subgenera: Astrophea, Decaloba, Deidamioides, Passiflora, and Tetrapathea. Passiflora cirrhiflora A. Juss. (subgenus Deidamioides) is an Amazonian species occurring in North Brazil, Venezuela, Guiana, Suriname, and French Guiana. Plastomes of the subgenus Deidamioides have demonstrated a complex pattern of evolution concerning phylogenetic aspects, size, rearrangements, gene losses, and pseudogenization. Therefore, we completely sequenced the plastome of P. cirrhiflora and characterized it in detail. The P. cirrhiflora plastome is a DNA molecule of 163,365 bp and contains 109 unique genes (75 protein-coding genes, 30 tRNAs, and 4 rRNAs). The infA and rps7 are pseudogenes in P. cirrhiiflora and the loss of the rps16 and rpl22 genes is a common feature shared by all plastomes of the genus Passiflora sequenced to date. Comparative analyses revealed a considerable structural variation at the IR borders, which consequently affected plastome size and structure within the subgenus Deidamioides. According to our prediction analysis, RNA editing sites are highly conserved within the subgenus Deidamioides, which significantly differs from the subgenus Passiflora. A total of 230 SSRs and six hotspots of nucleotide polymorphism were detected in the plastome of P. cirrhiiflora. Taken together, the complete plastome sequence of P. cirrhiflora is useful data for several studies in different areas such as phylogeny, genetic, and evolution.

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Section: Events Of Ir Expansion and Contraction Among Speciessupporting

confidence: 84%

Section: Events Of Ir Expansion and Contraction Among Speciessupporting

confidence: 79%

The complete plastome of Passiflora cirrhiflora A. Juss.: structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides

et al. 2020

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“…Among the beet plastomes, ycf1 is the most informative genic region (Figure 1A), which was also detected in other plant groups, such as the Tropaeolaceae, the orchids, and the Malvales (29–31). Additionally, the rpl22, matk, clpP1, ycf2, psaC and ndhF genes were reported to be highly divergent (29,31,32), which is mainly consistent with our findings. Here, the rrn-genes, ndhB (already classified as gene with low divergence (29,31)), rps12 and rps7 can be found among the gene loci with lower variance among the investigated species.…”

Section: Discussionmentioning

confidence: 84%

“…The intergenic regions are significantly less conserved containing more InDels and are therefore more suitable for phylogenies on a lower taxonomic level (22). Among the beet plastomes, ycf1 is the most informative genic region (Figure 1A), which was also detected in other plant groups, such as the Tropaeolaceae, the orchids, and the Malvales (29)(30)(31).…”

Section: Our Proposed Beet Whole-plastome Phylogeny Is Superior To Single Gene Phylogeniesmentioning

confidence: 99%

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

Sielemann

Pucker

Schmidt

et al. 2021

Preprint

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As the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes - traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution. We sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provide high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species. Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated. In conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.

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“…This species was listed as one of the plants with potential for economic use by the project "Plants for the Future -Southern Brazil" [5]. At the same time, T. pentaphyllum is endangered due to habitat degradation and over exploitation of edible tubers by local farms [5,9,10]. Despite the use potential of T. pentaphyllum, it remains remarkably understudied [11].…”

Section: Introductionmentioning

confidence: 99%

Seed Germination of the Herbaceous Vine Tropaeolum pentaphyllum Lam. (Tropaeolaceae): A Neglected Geophyte with High Agricultural Potential

Rogalski

Silva

Balestrin

et al. 2021

JEAI

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The objective of this study was to evaluate the seed germination of Tropaeolum pentaphyllum Lam., an endangered geophyte native of southern Brazil with agriculture potential due its edible tubers. Two experiments were carried out in 2017: germination of T. pentaphyllum under natural conditions and under controlled conditions. In the experiments under natural and controlled conditions, the germination of 1,100 and 100 seeds was evaluated, respectively. In the experiment under controlled conditions, two treatments (natural light and dark) were evaluated and each treatment contained 50 seeds. In the natural conditions experiment, in 2018 (first year), of the 1,100 seeds, 5.6% germinated and 76.5% persisted in the soil; and in 2019 (second year), 5.3% of the seeds germinated and no seeds remained in the soil. In natural conditions experiment, 10.9% of seeds germinated over two years. In controlled conditions experiment, in 2018 the germination in dark was higher (48%) compared to natural light (18%); and in 2019, despite the absence of statistical differences, the dark showed a higher value of germination (12%) in relation to natural light (6%). Over two years, dark treatment showed higher germination (60%) compared to natural light (24%) and no seeds remained in the substrate. The production of tubers in plants obtained by seed germination was 98.4% and 100%, in natural and controlled conditions, respectively. The highest germination rates occurred under dark conditions indicating that the species is preferential negative photoblastic. In addition, this species forms a seed bank in the soil, in which the seeds remained for a maximum of two years. The seed germination can contribute to the genetic diversity of crops and the production of seed-tubers, decreasing the collection of tubers in situ, contributing to the conservation and agricultural use of T. pentaphyllum.

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Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae)

Cited by 10 publications

References 99 publications

The complete plastome of Passiflora cirrhiflora A. Juss.: structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides

The complete plastome of Passiflora cirrhiflora A. Juss.: structural features, RNA editing sites, hotspots of nucleotide diversity and molecular markers within the subgenus Deidamioides

Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

Seed Germination of the Herbaceous Vine Tropaeolum pentaphyllum Lam. (Tropaeolaceae): A Neglected Geophyte with High Agricultural Potential

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