Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Ghanbari, Sina; Fakheri, Barat Ali; Naghavi, Mohammad Reza; Mahdinezhad, Nafiseh

doi:10.5010/jpb.2018.45.3.236

Cited by 5 publications

(8 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In previous studies (Ronsted et al, 2005;Huang et al, 2018), Fritillaria was partitioned into two clades, namely, subgenus Liliorhiza (including F. maximowiczii) and other subgenera, with Lilium nested in two Fritillaria clades based on a few plastid sequences. However, Fritillaria was monophyletic according to previous ITS-based studies (Hayashi and Kawano, 2000;Ronsted et al, 2005;Lee et al, 2011;Nursel, 2011;Gao et al, 2013;Ghanbari et al, 2018;Huang et al, 2018), which we confirmed here for our ITS-based inferences (Figure 1B). Also, Fritillaria is confirmed to be monophyletic (PP = 0.82, BS = 84) based on the plastome-based tree (Figure 1A).…”

Section: Plastome-based Inference Of Well-supported Phylogenetic Trees For Lilieaesupporting

confidence: 90%

“…Within Lilium, the plastome analyses split the ten sections of this genus into two clades (i.e., L1 and L2) with strong support. Our tree provided a better-supported picture of Lilium evolution than many previous analyses (Hayashi and Kawano, 2000;Gao et al, 2013;Du et al, 2014;Ghanbari et al, 2018) and supports a previous plastome study (Givnish et al, 2020). However, the subgeneric clades reconstructed by ITS were weakly supported, especially within Lilium (Figure 1B).…”

Section: Plastome-based Inference Of Well-supported Phylogenetic Trees For Lilieaesupporting

confidence: 89%

“…For Lilium , phylogenetic studies are often built on the seven morphological sections of Comber (1949) . Nonetheless, previous studies focused on partial clades and lack strong support, and so details of the infrageneric relationships for Fritillaria and Lilium remain controversial ( Gao et al, 2013 ; Du et al, 2014 ; Ghanbari et al, 2018 ; Tuyl et al, 2018 ; Givnish et al, 2020 ). Thus, with an increasing phylogenetic conflict being published, the resulting uncertainty in overall Lilieae phylogeny ( Huang et al, 2018 ; Kim and Kim, 2018 ) has limited further evolutionary study of the tribe.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Cai

Qin

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe. We sequenced 45 Liliaceae plastomes and combined them with publicly available data (for a total of 139 plastomes) to explore the systematics, origin, divergence, and evolution of Lilieae. Our taxon sampling covers all ten sections of Lilium, all Cardiocrinum species, three Notholirion species, and major phylogenetic clades of Fritillaria. Our phylogenetic analysis confirms the monophyly of major sections/subgenera of Lilium and Fritillaria with strong support. We dated the origin of Lilieae to the Eocene, with genera and species radiations inferred to have occurred in the Miocene. The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau (QTP): the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe. Ancestral-state reconstructions of the bulb component number (including bulblets and scales) show a strong correlation with the genus-level phylogenetic diversity in Lilieae. They also predict that the most recent common ancestor of Lilieae had bulbs with numerous bulblets. Based on these observations, we predicted that climatic oscillations associated with the QTP uplift played an important role in the evolution of the Lilieae bulb. Our findings provide a well-supported picture of evolutionary relationships and a useful framework for understanding the pathway of bulb evolution within Lilieae, contributing to a better understanding of the evolutionary history of lilies.

show abstract

Section: Plastome-based Inference Of Well-supported Phylogenetic Trees For Lilieaesupporting

confidence: 90%

Section: Plastome-based Inference Of Well-supported Phylogenetic Trees For Lilieaesupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Cai

Qin

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…Based on our observations, the haplogroup A is usually present in all continents, and the haplogroup B may similarly have originated from Asia (Fig. 3) (Ghanbari et al, 2018). The NJ tree was drawn by the Kimura distance (determination of distances aimed at building NJ tree using the MEGA 6.0 with the program defaults).…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic relationships of IranianAlliumspecies using thematK(cpDNA gene) region

et al. 2020

Self Cite

View full text Add to dashboard Cite

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were-1.5 for Tajima's D and-1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

show abstract

“…Some molecular based studies have been successfully carried out on Anaphalis and the Asteraceae Family by using molecular markers derived from nuclear ribosomal DNA (nrDNA), namely the Internal Transcribed Spacer (ITS) region [2]; and External Transcribed Spacers (ETS) [5]; and some use Simple Sequence Repeat (SSR) [12], [13]. The ITS area has proven to be a useful source of molecular information for genetic variation and phylogenetic studies in the Angiosperms plant group [14]; and RAPD marker for phylogenetic analysis [15], [16]. The use of Expressed Sequence-Tag Simple Sequence Repeat (EST-SSR) molecular markers has been successfully carried out in various studies on genetic diversity in several plant genera included in the Asteraceae Family [17], [18].…”

Section: Introductionmentioning

confidence: 99%

The Detection of Anaphalis spp. Genetic Diversity Based on Molecular Character (using ITS, ETS, and EST-SSR markers)

Ade

Hakim

Arumingtyas

et al. 2019

Int. J. Adv. Sci. Eng. Inf. Technol.

View full text Add to dashboard Cite

Anaphalis is the natural vegetation component in mountainous areas and is found in volcanic soils. Anaphalis is one of the species which existence is currently presumed to decrease and is feared to be extinct in nature. The purpose of this study was to detect genetic diversity of Anaphalis spp. in Bromo Tengger Semeru National Park (BTSNP) based on molecular characters by using ITS, ETS, and EST-SSR markers in supporting the conservation aspects of Anaphalis genetically. This research method was carried out by exploring the existence of Anaphalis populations, their coordinates marked by GPS, and leaf samples collected as a source of molecular analysis material. PCR products from ITS and ETS markers were sequenced, and the results' phylogenetic were analyzed using the MEGA6 program. PCR products from EST-SSR markers were performed by scoring DNA bands (allel) and both variations and genetics population were analyzed by using the POPGENE 1.32 program. Anaphalis populations found in BTSNP are Anaphalis javanica, A. longifolia, and A. viscida. The genetic diversity of Anaphalis spp. in BTSNP has polymorphism potential that is high enough, which is 57% (ITS) and 31% (ETS-partial), with a maximum likelihood phylogenetic tree topology which is monophyletic separated into four clusters consisting one cluster outgroup and three others being an ingroup. Whereas based on the genetic diversity value of the EST-SSR sequences in Anaphalis spp. in BTSNP shows that only A. longifolia populations in the Ranu Kumbolo area that have a high genetic diversity value (0.024) compared to the other two Anaphalis species. The highest genetic distance of Anaphalis spp. BTSNP in A. longifolia is found in the population of Penanjakan and Mt. Batok areas (0.040) with the smallest gene flow rate (0.428). Further research is needed to obtain a more complete picture of Anaphalis genetic diversity by using more molecular markers, bigger population numbers, more individuals and in bigger populations in other conservation areas in supporting the Anaphalis conservation strategy program.

show abstract

Evaluating phylogenetic relationships in the Lilium family using the ITS marker

Cited by 5 publications

References 17 publications

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes

Phylogenetic relationships of IranianAlliumspecies using thematK(cpDNA gene) region

The Detection of Anaphalis spp. Genetic Diversity Based on Molecular Character (using ITS, ETS, and EST-SSR markers)

Contact Info

Product

Resources

About