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Characterization of the complete chloroplast genome of the Taiwan alder Alnus formosana (Betulaceae) based on next-generation sequencing technology.

ABSTRACT: Alnus formosana (Betulaceae) is an important ecological and economic deciduous tree species widely distributed throughout subtropical regions of Taiwan province, China. At the present study, the complete chloroplast genome of A. formosana was assumbled using next-generation sequencing technology. The complete chloroplast sequence is 161,029 bp in length, which consisted of a large single copy (LSC, 89,720 bp) and a small single copy (SSC; 19,205 bp) separated a pair of inverted repeats (IRs; 26,052 bp). The overall guanine-cytosine (GC) content was 36.4%. A total of 131 genes were annotated, including 85 protein-coding genes, 37 tRNAs, eight rRNAs and one pseudogene (ψycf1). The phylogenetic analysis fully resolved A. formosana in a clade with A. japonica. The plastome of A. formosana will provide informative genomic resources for further phylogenetic application and genetic improvement.

SUBMITTER: Zhang X

PROVIDER: S-EPMC8425680 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Dataset Information

Characterization of the complete chloroplast genome of the Taiwan alder Alnus formosana (Betulaceae) based on next-generation sequencing technology.

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