Molecular Structure Analysis Of Complete Chloroplast Genomes Of Taxillus And Macrosolen Species From The Family Loranthaceae

Chloroplast is distinctly important organelle which has its own genome.Chloroplast genome contains valuable information and has been used as ideal research models,particularly for molecular markers,barcoding identification,plant evolution and comparative genomic studies.Given that parasitic plants have either lost some or all their photosynthetic capacity,many genes from some parasitic plants have been completely lost or pseudogenized.The genomic structure has also undergone major changes.Taxillus and Macrosolen,belonging to Loranthaceae family,are both hemiparasitic plants.Some species including Taxillus chinensis,T.sutchuenensis and Macrosolen cochinchinensis can be commonly used as herbal medicines.In the Chinese Pharmacopoeia,T.chinensis is recorded as "Sang Jisheng" to expel wind-damp,nourish liver and kidney,and treat some diseases,such as rheumatism,hypertension,and fetal irritability.In this study,we used the high-throughput sequencing technology to sequence,annotate and analyze the chloroplast genome sequences of four Taxillus species and three Macrosolen species.We also probed the effects of parasitic life on the variation of chloroplast genome.In addition,the chloroplast genome sequences were also used to determine the phylogenetic relationship among the Santalales.The main results are listed as follows:1.Chloroplast Genome Structures of Four Taxillus Species(1)The chloroplast genome sequences of T.chinensis,T.sutchuenensis,T.delavayi and T.thibetensis,are all circular molecules with quadripartite structure that are 121,363 bp,122,562 bp,119,941 bp and 122,286 bp in length,respectively.Each genome contains a large single-copy region(LSC)and a small single-copy region(SSC),which are separated by a pair of inverted repeats(IRs).(2)In the chloroplast genomes of T.chinensis and T.sutchuenensis,a total of 106 genes were identified in each genome which include 66 protein-coding genes,28 tRNAs,8 rRNAs,and 4 pseudogenes.In the chloroplast genomes of T.delavayi and T.thibetensis,a total of 109 genes including 69 protein-coding genes,29 tRNAs,eight rRNAs,and three pseudogenes were identified in each genome.(3)Compared with Nicotiana tabacum,genes encoding subunits of the NAD(P)H dehydrogenase complex(ndh genes)were lost from the chloroplast genome of T.chinensis and T.sutchuenensis,whereas three ribosomal protein genes,seven tRNA genes,four ycf genes,and initiation factor gene(infA)were also lost.Two ribosomal protein genes(rpl16 and rpl2)and the duplicate gene ycf 15 have also been pseudogenized.In the chloroplast genomes of T.delavayi and T.thibetensis,all ndh genes were lost,and two ribosomal protein genes,three tRNA genes,and four ycf genes were also lost.The rpl2 and ycf1 fragments at the border have been pseudogenized.(4)As a result of multiple sequence alignment,we observed that complete length of the SSC of these four species are much shorter than that of N.tabacum,and the lengths of SSC regions are about 3 kb smaller than that of the hemiparasitic plant Viscum minimum.The SSC regions of the chloroplast genomes of T.delavayi and T.thibetensis were inverted compared with T.chinensis,T.sutchuenensis,N.tabacum and V.minimum.2.Chloroplast Genome Structures of Macrosolen cochinchinensis,M.bibracteolatus,and M.tricolor(1)The chloroplast genome sequences of Macrosolen cochinchinensis,M.tricolor and M.bibracteolatus are 129,570 bp,126,621 bp and 127,169 bp in length,respectively,consisting of quadripartite structure.The GC contents of these three species are 37.3%,37.7%and 37.9%,respectively.(2)In the chloroplast genomes of M.cochinchinensis,M.tricolor,and M.bibracteolatus,a total of 113 genes were identified in each genome which include 68 protein-coding genes,35 tRNAs,eight rRNAs,and two pseudogenes.(3)Compared with N.tabacum,all ndh genes,three ribosomal protein genes,two tRNAs,three ycf genes and inf A gene of chloroplast genomes of three Macrosolen species were lost.(4)The results of multiple sequence alignment revealed that non-coding regions exhibit a higher divergence than coding regions.Two IR regions were less divergent than the LSC and SSC regions.The hypervariable region of LSC is trnF-trnM intergenic region.3.Phylogenetic Analysis of Seven speciesPhylogenetic trees were constructed based on 58 protein-coding genes commonly present in 16 species and matK genes.The result showed that the four Taxillus species were grouped with three Macrosolen species,and they were sister taxa with respect to Schoepfia jasminodora(Olacaceae).However,the three Viscum species grouped with Osyris alba(Santalaceae)and Champereia manillana(Opiliaceae).All phylogenetic results strongly support the theory that Loranthaceae and Viscaceae branched independently from one another.