Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species - PubMed (original) (raw)

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Ying Li et al. Sci Rep. 2017.

Abstract

Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1

Gene map of the complete chloroplast genome of T. chinensis. Genes on the inside of the circle are transcribed clockwise, while those outside are transcribed counter clockwise. The darker gray in the inner circle corresponds to GC content, whereas the lighter gray corresponds to AT content.

Figure 2

Gene map of the complete chloroplast genome of T. sutchuenensis. Genes on the inside of the circle are transcribed clockwise, while those outside are transcribed counter clockwise. The darker gray in the inner circle corresponds to GC content, whereas the lighter gray corresponds to AT content.

Figure 3

Comparison of the complete chloroplast genomes of six species using the MAUVE algorithm. Local collinear blocks are colored in this figure to indicate syntenic regions, while histograms within each block represent the degree of sequence similarity.

Figure 4

Codon content of 20 amino acid and stop codons in all protein-coding genes of the chloroplast genomes of two species. The histogram on the left-hand side of each amino acid shows codon usage within the T. chinensis chloroplast genome, while the right-hand side illustrates the genome of T. sutchuenensis.

Figure 5

Phylogenetic trees constructed using two methods based on two datasets from different species. (A) ML tree based on 54 protein-coding genes; (B) ML tree based on matK genes; (C) NJ tree based on 54 protein-coding genes; (D) NJ tree based on matK genes. Number at nodes are values for bootstrap support.

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Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species - PubMed (original) (raw)