Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis

Ali, M. Ajmal; Rahman, Mohammad Wahidur; Lee, Dong Kun; Hemaid, Fahad Al; Kambhar, Sidanand V.; Elangbam, Meena; Gurung, Arun Bahadur

doi:10.3329/bjpt.v27i2.50677

Cited by 4 publications

(2 citation statements)

References 21 publications

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“…Sequence information of both matK and rbcL genes was available for 30 species under 15 genera which was analyzed in the present study (Table 1). Application of NCBI public sequence data alone to resolve phylogenetic relationships was supported by several studies (Gholizadeh et al, 2013;Ali et al, 2020;Aykut, 2020). Several species including Arenga pinnata (Wurmb) Merr., Calamus latifolius Roxb., Corypha taliera Roxb., Daemonorops jenkinsiana (Griff.)…”

Section: Molecular Dating Analysesmentioning

confidence: 99%

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

Ahmed,

Rahman,

Ali

et al. 2023

Bangladesh J. Plant Taxon

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A molecular phylogenetic investigation was undertaken for 30 species belonging to 15 genera of the palm family Arecaceae in Bangladesh to infer evolutionary relationships and molecular dating utilizing plastid-based matK and rbcL genes through multifaceted-algorithm driven approaches with Neighbor-Joining, Maximum-Likelihood, and Bayesian Inference methods. The study revealed that matK has better species discrimination efficiency than rbcL gene due to its highly variable nature. Transition/transversion bias test corroborated this finding as matK showed higher bias (2.632) than rbcL (2.235). Nucleotide substitution patterns were visualized via HYPERMUT program, which unveiled higher variability in matK and lower variability in rbcL alignment. Phylogenetic trees constructed with matK revealed monophyletic nature of origin for all the three subfamilies, viz. Arecoideae, Coryphoideae and Calamoideae, while rbcL trees exhibited polyphyly for Coryphoideae and monophyly for Arecoideae and Calamoideae. All the nine tribes belonging to three subfamilies demonstrated monophyletic nature in matK trees. Bootstrap support and Bayesian posterior probability were found to be higher in matK topologies than that of rbcL. The molecular clock test unraveled an equal evolutionary rate for matK and unequal rate for rbcL sequences. Molecular dating approach unveiled Calamoideae to be the most ancient subfamily (65.75 MYA) among the three subfamilies that originated during the Late Cretaceous period in the Mesozoic era, whereas Coryphoideae and Arecoideae were found to have originated in the Cenozoic era. Bangladesh J. Plant Taxon. 30(2): 213-232, 2023 (December)

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Section: Molecular Dating Analysesmentioning

confidence: 99%

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

Ahmed,

Rahman,

Ali

et al. 2023

Bangladesh J. Plant Taxon

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“…In Euphorbiaceae (rosids: Malpighiales), a nuclear phylogeny was reported for the genus Euphorbia (Villaverde et al, 2018). Furthermore, the phylogeny of the Krameriaceae (rosids: Zygophyllales) genus Krameria (Ali et al, 2020) and the Melastomataceae (rosids: Myrtales) genus Memecylon (Amarasinghe et al, 2021) was analyzed using nuclear genes.…”

Section: Angiosperm Phylogenomics Using Nuclear Genesmentioning

confidence: 99%

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Zhang,

2024

JIPB

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Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,” hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next‐generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.

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Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication

Ali

2021

Saudi Journal of Biological Sciences

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The recent massive development in the next-generation sequencing platforms and bioinformatics tools including cloud based computing have proven extremely useful in understanding the deeper-level phylogenetic relationships of angiosperms. The present phylotranscriptomic analyses address the poorly known evolutionary relationships of the order Dilleniales to order of the other angiosperms using the minimum evolution method. The analyses revealed the nesting of the representative taxon of Dilleniales in the MPT but distinct from the representative of the order Santalales, Caryophyllales, Asterales, Cornales, Ericales, Lamiales, Saxifragales, Fabales, Malvales, Vitales and Berberidopsidales.

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Dissecting molecular evolutionary relationship of Krameriaceae inferred from phylotranscriptomic analysis

Cited by 4 publications

References 21 publications

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

Molecular Phylogenetics and Molecular Dating of Arecaceae In Bangladesh Inferred from Matk and Rbcl Genes

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Phylotranscriptomic analysis of Dillenia indica L. (Dilleniales, Dilleniaceae) and its systematics implication

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