Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae

Abstract

Chloroplast genomes of plants are highly conserved in both gene order and gene content, are maternally inherited, and have a lower rate of evolution. Chloroplast genomes are considered to be good models for testing lineage-specific molecular evolution. In this study, we use Schisandraceae as an example to generate insights into the overall evolutionary dynamics in chloroplast genomes and to establish the phylogenetic relationship of Schisandraceae based on chloroplast genome data using phylogenomic analysis. By comparing three Schisandraceae chloroplast genomes, we demonstrate that the gene order, gene content, and length of chloroplast genomes in Schisandraceae are highly conserved but experience dynamic evolution among species. The number of repeat variations were detected, and the Schisandraceae chloroplast genome was revealed as unusual in having a 10 kb contraction of the IR due to the genome size variations compared with other angiosperms. Phylogenomic analysis based on 82 protein-coding genes from 66 plant taxa clearly elucidated that Schisandraceae is a sister to a clade that includes magnoliids, monocots, and eudicots within angiosperms. As to genus relationships within Schisandraceae, Kadsura and Schisandra formed a monophyletic clade which was sister to Illicium.

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae

“…The GC content in the IR region was higher than both LSC and SSC regions in all examined Paphiopedilum plastomes. This result agreed with previous studies [6,7,26,27]. The presence of four ribosomal RNA (rRNA) genes is considered to be the reason for high GC contents in the IR regions [6,26].…”

“…This result agreed with previous studies [6,7,26,27]. The presence of four ribosomal RNA (rRNA) genes is considered to be the reason for high GC contents in the IR regions [6,26]. However, another hypothesis proposed that the higher GC content evolution in IR regions does not relate to natural selection but to GC-biased gene conversion (gBGC) [7,27].…”

DNA Fingerprinting and Species Identification Uncovers the Genetic Diversity of Katsouni Pea in the Greek Islands Amorgos and Schinoussa

“…Herein, the inability of most of the barcoding markers to discriminate samples at the species level, being not variable enough to resolve phylogeny of the genus, is probably due to the conserved chloroplast sequences and the low mutation rate [53]. The inability to discriminate among the P. abyssinicum, P. sativum subsp.…”

Why the Monophyly of Nymphaeaceae Currently Remains Indeterminate: An Assessment Based on Gene-Wise Plastid Phylogenomics

“…The latter scenario appears to be the case when attempting to reconstruct the phylogenetic relationships of Nymphaeaceae and Cabombaceae while using members of its sister clade Hydatellaceae as outgroup. A high amount of character change exists between the ingroup (Nymphaeaceae and Cabombaceae) and its potential outgroup (Hydatellaceae), as evidenced by the large patristic distance between the two groups [13,14]. In fact, [13] (Fig.…”

“…The exact phylogenetic relationships within Nymphaeales remain controversial, primarily due to the uncertain position of the genus Nuphar. Two recent plastid phylogenomic investigations have recovered Nuphar apart from the other Nymphaeaceae [13,14], whereas older molecular phylogenetic studies have inferred the genus as the earliest diverging lineage of the family, albeit with mixed phylogenetic signal [4,15,16]. The precise phylogenetic position of Nuphar affects the taxonomic status of Nymphaeaceae as a monophyletic group (Fig.…”