The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement...

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Bibliographic Details
Published in:PloS one 2015-06, Vol.10 (6), p.e0129347-e0129347
Main Authors: Yao, Xiaohong, Tang, Ping, Li, Zuozhou, Li, Dawei, Liu, Yifei, Huang, Hongwen
Format: Article
Language:English
Subjects:
Actinidia
Actinidia - genetics
Actinidia chinensis
Actinidiaceae
Actinidiaceae - classification
Actinidiaceae - genetics
Analysis
Angiosperms
Botanical gardens
Camellia sinensis
Chloroplast Proteins - classification
Chloroplast Proteins - genetics
Chloroplasts
Comparative analysis
Contraction
Deoxyribonucleic acid
DNA
DNA sequencing
DNA, Chloroplast - chemistry
DNA, Chloroplast - genetics
Economic analysis
Economic planning
Evolution
Flowers & plants
Gene duplication
Gene sequencing
Genes
Genes, Chloroplast - genetics
Genetic engineering
Genetic improvement
Genome, Chloroplast - genetics
Genome, Plant - genetics
Genomes
Genomics
Germplasm
Inverted repeat
Kiwifruit
Laboratories
Molecular Sequence Data
Mutation
Nuclei
Nucleotide sequence
Phylogenetics
Phylogeny
PsbA gene
Repetitive Sequences, Nucleic Acid - genetics
Reproduction (copying)
Ribonucleic acid
RNA
rRNA
Sequence Analysis, DNA
Transfer RNA
tRNA
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Summary:Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0129347