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

Ying Li,Ying-Xian Cui,Zhi-Chao Xu,Jing-Yuan Song,Jian-Guo Zhou,Yong-Hua Li,Bao-Zhong Duan,Hui Yao,Xin-Lian Chen

doi:10.1038/s41598-017-13401-4

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.

Highlights

The chloroplast is a key plant cell organelle that carries out photosynthesis[1]
We report the complete chloroplast genome of T. chinensis and T. sutchuenensis, which are the first two sequences completed within Loranthaceae
Results show that the chloroplast genome sequence of T. chinensis is a circular molecule that is 121,363 bp in length, which can be divided into a large single-copy (LSC) region of 70,357 bp and a small single-copy (SSC) region of 6,082 bp, and separated by a pair of inverted repeats (IRa and IRb) each 22,462 bp in length (Fig. 1)

Summary

Results

Chloroplast Genome Structures of T. chinensis and T. sutchuenensis. Results show that the chloroplast genome sequence of T. chinensis is a circular molecule that is 121,363 bp in length, which can be divided into a large single-copy (LSC) region of 70,357 bp and a small single-copy (SSC) region of 6,082 bp, and separated by a pair of inverted repeats (IRa and IRb) each 22,462 bp in length (Fig. 1). The complete and correct chloroplast genome sequences of T. chinensis and T. sutchuenensis were deposited in GenBank under accession numbers KY996492 and KY996493, respectively Data reveal that both species have a GC content of 37.3%, which is unevenly distributed across the whole chloroplast genome. In both cases, the GC content of the IR regions exhibits the highest values across the complete chloroplast genome, 43.0% in T. chinensis and 42.8% in T. sutchuenensis, respectively. The calculations for the codon usage of protein-coding genes within T. chinensis and T. sutchuenensis chloroplast genomes are summarized in Fig. 4 and Supplementary Table S3. 195 and 198 SSRs are identified within the chloroplast genomes of T. chinensis and T. sutchuenensis, respectively (Table 3; Supplementary Tables S4–S5), which mainly comprise mononucleotide repeats encountered 146 and 139 times in each case. All four phylogenetic trees showed that T. chinensis and T. sutchuenensis are sister taxa with respect to S. jasminodora (Olacaceae), whereas the three species within genus Viscum group with Osyris alba (Santalaceae) and all Santalales species are clustered within a lineage distinct from the outgroup

Discussion

Conclusions

Materials and Methods