Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

• Published in: Scientific reports Vol. 14; no. 1; pp. 24808 - 10
• Main Authors: Zahra, Syeda Anber, Iqbal, Javed, Abbasi, Banzeer Ahsan, Kanwal, Sobia, Alwahibi, Mona S., Elshikh, Mohamed S., Rizwan, Muhammad, Iqbal, Rashid, Mahmood, Tariq
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22-10-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 3D protein modeling; 631/208; 631/449; Amino Acid Sequence; Amino acids; Asteraceae; Asteraceae - classification; Asteraceae - genetics; Chloroplasts; Evolution; Evolution, Molecular; Flowering; Flowering plants; Genetic analysis; Genetic distance; Genetic diversity; Genetic relationship; Genetic variability; Genetic Variation; Humanities and Social Sciences; Molecular evolutionary genetic analysis; multidisciplinary; Nucleotide sequence; Phylogenetics; Phylogeny; Phylogram; Plant Proteins - genetics; Protein structure; Proteins; Ribosomal Proteins - genetics; rps 11; Science; Science (multidisciplinary); Species; Species diversity; Statistical analysis; 11; Molecular evolutionary genetic analysis; 3D protein modeling; Genetic variability; Phylogram; rps 11; Asteraceae
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-75991-0

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the
rps
-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (
rps
11). Nearly 417 bp of
rps
11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for
rps
11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for
rps
11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the
rps
11 protein structures of
Tagetes minuta
,
Xanthium strumarium
,
Lactuca sativa
and
Chrysanthemum indicum
have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the
rps
11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.