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.
Highlights
The family Betulaceae in the order Fagales consist of approximately 100∼150 species of trees and shrubs that distributed in the temperate zone of the Northern Hemisphere, with a few species spreading to South America and only one species (Alnus glutinosa (L.) Gaertn) occurring in Africa (Kubitzki, Rohwer & Bittrich, 1993)
Illumina paired-end (2 × 150 bp) sequencing generated large datasets for each species, with 8,683,726 (Ostryopsis davidiana), 22,450,682 (Corylus wangii), and 27,361,376 (Alnus cremastogyne) paired-end reads mapped to the reference genome sequences, resulting 777×, 132×, and 785× coverage across the three cp genomes
The results indicated that the quality of cp genome sequencing and assembly was very high
Summary
The family Betulaceae in the order Fagales consist of approximately 100∼150 species of trees and shrubs that distributed in the temperate zone of the Northern Hemisphere, with a few species spreading to South America and only one species (Alnus glutinosa (L.) Gaertn) occurring in Africa (Kubitzki, Rohwer & Bittrich, 1993). The generic relationships within the family have subjected to various controversies In previous studies, both morphological taxonomy and molecular phylogenies have generally recognized two main lineages in Betulaceae, treated either as two tribes (Coryleae and Betuleae) (Bousquet, Strauss & Li, 1992; Crane, 1989) or two subfamilies (Coryloideae and Betuloideae) (Furlow, 1990; Bousquet, Strauss & Li, 1992; Chen, Manchester & Sun, 1999; Forest et al, 2005). This research elucidates the potential of chloroplast genome sequences in the application of developing molecular markers, studying evolutionary relationships and historical dynamic of Betulaceae. It 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
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