Plastome structure, phylogenomic analyses and molecular dating of Arecaceae

Abstract

Arecaceae is a species-rich clade of Arecales, while also being regarded as a morphologically diverse angiosperm family with numerous species having significant economic, medicinal, and ornamental value. Although in-depth studies focused on the chloroplast structure of Arecaceae, as well as inferring phylogenetic relationships using gene fragments, have been reported in recent years, a comprehensive analysis of the chloroplast structure of Arecaceae is still needed. Here we perform a comprehensive analysis of the structural features of the chloroplast genome of Arecaceae, compare the variability of gene sequences, infer phylogenetic relationships, estimate species divergence times, and reconstruct ancestral morphological traits. In this study, 74 chloroplast genomes of Arecaceae were obtained, covering five subfamilies. The results show that all chloroplast genomes possess a typical tetrad structure ranging in size between 153,806-160,122 bp, with a total of 130-137 genes, including 76-82 protein-coding genes, 29-32 tRNA genes, and 4 rRNA genes. Additionally, the total GC content was between 36.9-37.7%. Analysis of the SC/IR boundary indicated that the IR region underwent expansion or contraction. Phylogenetic relationships indicate that all five subfamilies in Arecaceae are monophyletic and that Ceroxyloideae and Arecoideae are sister groups (BS/PP = 100/1). The results of molecular dating indicate that the age of the crown group of Arecaceae is likely to be 96.60 [84.90-107.60] Ma, while the age of the stem group is 102.40 [93.44-111.17] Ma. Reconstruction of ancestral traits indicate that the ancestral characteristics of the family include monoecious plants, one seed, six stamens, and a smooth pericarp.

A plastid phylogenomic framework for the palm family (Arecaceae)

“…S1). Our results are largely congruent with previous plastid phylogenetic analyses [47,48,57,58,64] but provide higher support for some tribal and generic relationships, especially those among Geonomateae, Leopoldinieae, Manicarieae, and Pelagodoxeae (Fig. 1; Additional files 4, 5: Figs.…”

“…S2). However, this sister relationship was strongly supported in previous studies based on both nuclear genomic data [39] and plastome data [48,58], as well as in a recent study based on a combined analysis of three nuclear regions (RPB2, CISP4, WRKY6) and one plastid region (trnT-trnD) [75]. Relationships among subtribes and genera of the family were also mostly resolved with moderate or high support (Fig.…”

“…Phylogenetic topologies among all the five subfamilies, among major clades within Arecoideae, among most tribes within Coryphoideae, and among most subtribes and genera in the family were consistent in analyses based on both plastid (Fig. 1) [47,48,58] and nuclear data [39,49,59,60,63,66,78] and also mostly obtained strong supported. Additionally, although the sister relationships between Phoeniceae and Trachycarpeae within Coryphoideae recovered in the plastome tree (Fig.…”

“…35.5% species-level taxon sampling and 13 DNA markers (9 plastid and 4 nuclear regions), low support was obtained for relationships among some tribes and subtribes as well [25]. Seventyfour plastid genomes of 54 palm genera representing five subfamilies and 19 tribes were analyzed by Chen et al [58], and relationships among all of them were mostly resolved with high support, but multiple tribes within the largest subfamily Arecoideae were not included. In a recent phylogenomic study of 2333 angiosperm genera based on an analysis of 353 nuclear genes, 67 genera representing 26 palm tribes and all the five palm subfamilies were included, the subfamily-level relationships and most tribal-level relationships were highly supported except some tribal-level relationships within Arecoideae were resolved with weak support [59].…”

“…Thus, plastid phylogenomics have been adopted extensively in recent studies of plant lineages both at deep and shallow taxonomic levels, such as in liverworts [68], ferns [69,70], gymnosperms [71], and angiosperms [5,10,13,31,34,37,[72][73][74], providing critical insights into the recalcitrant phylogenetic relationships within these groups. In contrast with the continuously increasing body of nuclear-based palm phylogenomic studies [39,41,49,[59][60][61][62][63], a comprehensive generic-level plastid phylogenomic study of the family is still lacking [47,58]. Here, we conducted a plastid phylogenomic analysis of palms based on a nearly complete generic-level sampling and aimed at (1) shedding new light on the relationships among tribes, subtribes, and genera of palms and (2) evaluating how plastome and nuclear histories differ across the family.…”