Research Paper

Lowest copy nuclear genes in disentangling plant molecular systematics

Anjan Hazra, Sriparna Bhowmick, Chandan Sengupta, Sauren Das

Published on: 17 August 2020

Page: 413 - 422

DOI: 10.6165/tai.2020.65.413

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2020 vol.65 no.4 pp.413-422


In recent years, low copy nuclear genes became a promising choice in plant phylogeny and systematic studies for being bi-parentally inherited and highly variable, thus possessing more phylogenetically informative sites in contrast to widely used organellar genes. Here, a set of nuclear genes has been fished out from the plant genome database targeting their single copy presence in whole genomes of most of the taxa. Low copy genes, that are yet to be included in molecular phylogenetic studies of plants, were selected. All group of green plants from algae to angiosperm has been considered for validating these markers towards determining both species level and deep lineage hierarchy. The reconstructed phylogeny with selected genes, in present work, exhibited good resolution up to family level with high statistical support. Moreover, NAD, PS54, P4H, CDIPT, and GTF could also serve well up to higher rank clustering. Concatenated species tree through best predicted substitution model with and without third codon position corroborated the prospects of nuclear gene-based phylogeny with some incongruences in the hierarchy. The study acclaimed fourteen low copy nuclear genes concerning the determination of their efficacy toward inferring the taxonomic relationship of green plants which might be used in further molecular systematics and population genetic studies.

Keyword: Angiosperm, low copy nuclear genes, molecular systematics, phylogenomics, plants