The complete chloroplast genomes of three Betulaceae species: implications for molecular phylogeny and historical biogeography

Abstract

BackgroundPrevious phylogenetic conclusions on the family Betulaceae were based on either morphological characters or traditional single loci, which may indicate some limitations. The chloroplast genome contains rich polymorphism information, which is very suitable for phylogenetic studies. Thus, we sequenced the chloroplast genome sequences of three Betulaceae species and performed multiple analyses to investigate the genome variation, resolve the phylogenetic relationships, and clarify the divergence history.MethodsChloroplast genomes were sequenced using the high-throughput sequencing. A comparative genomic analysis was conducted to examine the global genome variation and screen the hotspots. Three chloroplast partitions were used to reconstruct the phylogenetic relationships using Maximum Likelihood and Bayesian Inference approaches. Then, molecular dating and biogeographic inferences were conducted based on the whole chloroplast genome data.ResultsBetulaceae chloroplast genomes consisted of a small single-copy region and a large single copy region, and two copies of inverted repeat regions. Nine hotspots can be used as potential DNA barcodes for species delimitation. Phylogenies strongly supported the division of Betulaceae into two subfamilies: Coryloideae and Betuloideae. The phylogenetic position of Ostryopsis davidiana was controversial among different datasets. The divergence time between subfamily Coryloideae and Betuloideae was about 70.49 Mya, and all six extant genera were inferred to have diverged fully by the middle Oligocene. Betulaceae ancestors were probably originated from the ancient Laurasia.DiscussionsThis research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae.It also reveals the advantages of using chloroplast genome data to illuminate those phylogenies that have not been well solved yet by traditional approaches in other plants.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…When less genomic resources are available for revealing divergence hotspot regions, the oligonucleotide repeats might be utilized as a substitute for identifying polymorphic regions (Ahmed et al, 2012; Ahmad, 2014). The current study results of oligonucleotide repeats are similar to the previously reported results of Nicotiana species and other angiosperm plastome studies (Asaf et al, 2016; Yang et al, 2019). Thus, the presence of both the high divergence regions in IGS and oligonucleotide repeats suggest that these regions are suitable for the development of markers to demonstrate phylogenetics relationships.…”

The chloroplast genome sequence of Dipteryx alata Vog. (Fabaceae: Papilionoideae): genomic features and comparative analysis with other legume genomes

“…The content and order of genes are highly conserved in most cp genomes (Ruhlman and Jansen 2014). Little or no recombination events are usually detected in the cp genome that also is subjected to a slow mutation rate (Yang et al 2019), although some species of the Fabaceae family, which are exceptions, have a rapid mutation rate, rearrangements and gene losses (Cai et al 2008;Magee et al 2010). In general, chloroplasts have sufficient ribosomal RNA (rRNA) and transporter RNA (tRNA) genes to compose the translation machinery for expression of their own genes (Wicke et al 2011).…”

Peer Review #1 of "Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) (v0.2)"

“…otophora (Asaf et al, 2016). In all the species of Nicotiana, the LSC region contained a greater amount of SSRs in comparison to SSC and IR, which has also been demonstrated in other studies of angiosperm plastid genomes ( Asaf et al, 2016;Shahzadi et al, 2019;Mehmood et al, 2019, Yang et al, 2019. To understand molecular evolution, it is important to analyze nucleotide substitution rates (Muse & Gaut, 1994); in plastid genomes LSC and SSC regions are more prone to substitutions and indels, whereas the IRs are more conserved (Ahmed et al, 2012;Abdullah et al, 2019b).…”