Complete chloroplast genome sequence of holoparasite Cistanche deserticola (Orobanchaceae) reveals gene loss and horizontal gene transfer from its host Haloxylon ammodendron (Chenopodiaceae)

BACKGROUND

The central function of chloroplasts is to carry out photosynthesis, and its gene content and structure are highly conserved across land plants. Parasitic plants, which have reduced photosynthetic ability, suffer gene losses from the chloroplast (cp) genome accompanied by the relaxation of selective constraints. Compared with the rapid rise in the number of cp genome sequences of photosynthetic organisms, there are limited data sets from parasitic plants. PRINCIPAL FINDINGS/SIGNIFICANCE: Here we report the complete sequence of the cp genome of Cistanche deserticola, a holoparasitic desert species belonging to the family Orobanchaceae. The cp genome of C. deserticola is greatly reduced both in size (102,657 bp) and in gene content, indicating that all genes required for photosynthesis suffer from gene loss and pseudogenization, except for psbM. The striking difference from other holoparasitic plants is that it retains almost a full set of tRNA genes, and it has lower dN/dS for most genes than another close holoparasitic plant, E. virginiana, suggesting that Cistanche deserticola has undergone fewer losses, either due to a reduced level of holoparasitism, or to a recent switch to this life history. We also found that the rpoC2 gene was present in two copies within C. deserticola. Its own copy has much shortened and turned out to be a pseudogene. Another copy, which was not located in its cp genome, was a homolog of the host plant, Haloxylon ammodendron (Chenopodiaceae), suggesting that it was acquired from its host via a horizontal gene transfer.

Chemical and genetic discrimination of Cistanches Herba based on UPLC-QTOF/MS and DNA barcoding

Cistanches Herba (Rou Cong Rong), known as "Ginseng of the desert", has a striking curative effect on strength and nourishment, especially in kidney reinforcement to strengthen yang. However, the two plant origins of Cistanches Herba, Cistanche deserticola and Cistanche tubulosa, vary in terms of pharmacological action and chemical components. To discriminate the plant origin of Cistanches Herba, a combined method system of chemical and genetic--UPLC-QTOF/MS technology and DNA barcoding--were firstly employed in this study. The results indicated that three potential marker compounds (isomer of campneoside II, cistanoside C, and cistanoside A) were obtained to discriminate the two origins by PCA and OPLS-DA analyses. DNA barcoding enabled to differentiate two origins accurately. NJ tree showed that two origins clustered into two clades. Our findings demonstrate that the two origins of Cistanches Herba possess different chemical compositions and genetic variation. This is the first reported evaluation of two origins of Cistanches Herba, and the finding will facilitate quality control and its clinical application.

Metabolome and transcriptome profiling reveals quality variation and underlying regulation of three ecotypes for Cistanche deserticola

Cistanche deserticola is a plant used both as food and medicine. We are interested in understanding how C. deserticola responds to environmental conditions. Samples were collected from three ecotypes grown in saline-alkali land, grassland and sandy land. Transcriptome and metabolome analysis were performed by using RNA-seq and LC-ESI-MS/MS. Among 578 metabolites identified, 218, 209 and 215 compounds were found differentially produced among the three ecotypes. Particularly, 2'-acetylacteoside, belonging to phenylethanoid glycosides (PhGs) is the most significantly differentially produced with a VIP > 0.5 and fold change > 2, representing a potential chemical marker to distinguish the three ecotypes. RNA-Seq analysis revealed 52,043 unigenes, and 947, 632 and 97 of them were found differentially expressed among the three ecotypes. Analysis of the correlation between the metabolome profiles and transcriptome profiles among three ecotypes identified that the 12 key genes related to PhGs biosynthesis were differentially expressed. Particularly, the expression of PAL, ALDH and GOT genes were significantly up-regulated in saline-alkali land compared to the other two. In summary, we found PhGs content was higher in saline-alkali land compared with other ecotypes. This is likely due to the up-regulation of the PhGs biosynthetic genes in response to the saline-alkali conditions.

Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes

The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.

RNA-Seq Based De Novo Transcriptome Assembly and Gene Discovery of Cistanche deserticola Fleshy Stem

Backgrounds

Cistanche deserticola is a completely non-photosynthetic parasitic plant with great medicinal value and mainly distributed in desert of Northwest China. Its dried fleshy stem is a crucial tonic in traditional Chinese medicine with roles of mainly improving male sexual function and strengthening immunity, but few mechanistic studies have been conducted partly due to the lack of genomic and transcriptomic resources.

Results

In this study, we performed deep transcriptome sequencing in fleshy stem of C. deserticola, and about 80 million reads were generated using Illumina pair-end sequencing on HiSeq2000 platform. Using trinity assembler, we obtained 95,787 transcript sequences with transcript lengths ranging from 200bp to 15,698bp, having an average length of 950 bases and the N50 length of 1,519 bases. 63,957 transcripts were identified actively expressed with FPKM ≥ 0.5, in which 30,098 transcripts were annotated with gene descriptions or gene ontology terms by sequence similarity analyses against several public databases (Uniprot, NR and Nt at NCBI, and KEGG). Furthermore, we identified key enzyme genes involved in biosynthesis of lignin and phenylethanoid glycosides (PhGs) which are known to be the primary active ingredients. Four phenylalanine ammonia-lyase (PAL) genes, the first key enzyme in lignin and PhG biosynthesis, were identified based on sequences comparison and phylogenetic analysis. Two biosynthesis pathways of PhGs were also proposed for the first time.

Conclusions

In all, we completed a global analysis of the C. deserticola fleshy stem transcriptome using RNA-seq technology. A collection of enzyme genes related to biosynthesis of lignin and phenylethanoid glysides were identified from the assembled and annotated transcripts, and the gene family of PAL was also predicted. The sequence data from this study will provide a valuable resource for conducting future phenylethanoid glysides biosynthesis researches and functional genomic studies in this important medicinal plant.

Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification

BACKGROUND

Cistanche is an important genus of Orobanchaceae, with critical medicinal, economic, and desertification control values. However, the phylogenetic relationships of Cistanche genus remained obscure. To date, no effective molecular markers have been reported to discriminate effectively the Cistanche closely related species reported here. In this study, we obtained and characterized the plastomes of four Cistanche species from China, to clarify the phylogenetic relationship within the genus, and to develop molecular markers for species discrimination.  RESULTS: Four Cistanche species (Cistanche deserticola, Cistanche salsa, Cistanche tubulosa and Cistanche sinensis), were deep-sequenced with Illumina. Their plastomes were assembled using SPAdes and annotated using CPGAVAS2. The plastic genomes were analyzed in detail, finding that all showed the conserved quadripartite structure (LSC-IR-SSC-IR) and with full sizes ranging from 75 to 111 Kbp. We observed a significant contraction of small single copy region (SSC, ranging from 0.4-29 Kbp) and expansion of inverted repeat region (IR, ranging from 6-30 Kbp), with C. deserticola and C. salsa showing the smallest SSCs with only one gene (rpl32). Compared with other Orobanchaceae species, Cistanche species showed extremely high rates of gene loss and pseudogenization, as reported for other parasitic Orobanchaceae species. Furthermore, analysis of sequence divergence on protein-coding genes showed the three genes (rpl22, clpP and ycf2) had undergone positive selection in the Cistanche species under study. In addition, by comparison of all available Cistanche plastomes we found 25 highly divergent intergenic spacer (IGS) regions that were used to predict two DNA barcode markers (Cis-mk01 and Cis-mk02 based on IGS region trnR-ACG-trnN-GUU) and eleven specific DNA barcode markers using Ecoprimer software. Experimental validation showed 100% species discrimination success rate with both type of markers.

CONCLUSION

Our findings have shown that Cistanche species are an ideal model to investigate the structure variation, gene loss and pseudogenization during the process of plastome evolution in parasitic species, providing new insights into the evolutionary relationships among the Cistanche species. In addition, the developed DNA barcodes markers allow the proper species identification, ensuring the effective and safe use of Cistanche species as medicinal products.

[Study on genetic diversity of natural and cultivated Cistanche tubulosa]

OBJECTIVE

To determine the genetic diversity of natural and cultivated Cistanche tubulosa.

METHOD

123 individuals of six populations of C. tubulosa, including four natural populations and two cultivated ones, were analyzed by random amplified polymorphic DNA (RAPD) markers to determine the genetic variations among the populations.

RESULT

A total of 87 loci (including 24 polymorphic loci) were amplified using 10 random primers. The average percentage of polymorphic loci (PPL) was 27.59 in the natural populations. The PPL between natural populations are 19.54 to 25.29. Of the four natural populations, Andi' er population had highest PPL (25.29). The two cultivated populations had low PPL (13.79 and 11.49). Cluster analysis using UPGMA revealed that populations of natural and cultivated were separated into two groups, the four natural populations clustered as one group and the two cultivated populations clustered as another group, indicating that the natural and cultivated populations had obvious differentiation.

CONCLUSION

In view of the low genetic diversity of the cultivated C. tubulosa, we strongly suggested that the natural populations should be conserved in particular.

[Study on genetic diversity of herba Cistanches by RAPD]

OBJECTIVE

To determine the genetic diversity of Cistanche species.

METHOD

Two populations of Cistanche deserticola and four populations of C. tubulosa were analyzed by random amplified polymorphic DNA (RAPD) markers.

RESULT

A total of 76 and 87 loci were amplified using 10 random primers each other. The average percentage of polymorphic loci of C. deserticola was 47.37%. The PPL were 39.47% and 35.53% for two populations. Average Nei's gene diversity was 0.1358, Shannon' s genetic diversity was 0.2072, and Gst was 0.2546. The average PPL of C. tubulosa was 27.59%. It was 19.54% to 25.29% in different populations and Andi'er population had the highest. Average Nei's gene diversity was 0.0823, and Shannon' s genetic diversity was 0.125 8, Cst was 0.175 5.

CONCLUSION

The diversity of Cistanche deserticola is higher than that of C. tubulosa, but both has differentiation among populations, C. deserticola has already separated itself into two different ecotypes.

[Analysis on Cistanche tubulosa that parasites on different Tamarixs by RAPD]

OBJECTIVE

To study genetic difference of Cistanche tubulosa that parasites on different Tamarixs and give a reference to select host of C. tubulosa.

METHOD

Sixteen selected primers by random amplified polymorphic DNA (RAPD) markers were used to analyze genetic distance of C. tubulosa that parasites on eight different hosts.

RESULT

Sixty-six point seven percent of the total bands were polymorphic, that proved the genetic diversity level in different C. tubulosa types was relatively high, especially the two that parasites on Tamarix hispida and T. chinensis. Cultural areas had more remarkable influence on genetic distance of Cistanche tubulosa than the hosts, and introduction was helpful to maintain the more genetic diversity in different C. tubulosa types. Genetic difference in different C. tubulosa types was far less than that between different species in Cistanche.

CONCLUSION

C. tubulosa types which parasite on different Tamarixs have high genetic diversity.

[Morphotype diversity of Cistanche deserticola]

OBJECTIVE

To provide theoretical basis for selecting high quality seeds by studying the modality diversity of Cistanche deserticola.

METHOD

Four populations were collected in the field and its biodiversity was studied by comparative morphoaanatory to identify its mutation of nutrition organ and reproduction organ in laboratory and herbarium.

RESULT AND CONCLUSION

There are several types of C. deserticola that come from different types, which results in the difference in pharmacody and effect of medicine.

Identification of Cistanche species (Orobanchaceae) based on sequences of the plastid psbA-trnH intergenic region

The dried succulent stems of Cistanche (Cistanche deserticola Y. C. Ma and Cistanche tubulosa Wight.) are one of the most widely used components of traditional Chinese medicines. However, it is often confused and substituted with the roots of Orobanche pycnostachya, Boschniakia rossica (Cham. & Schltdl.) Standl., Cistanche sinensis Beck, and Cistanche salsa (C. A. Mey.) Beck. In this study, we identified psbA-trnH regions from species and tested their suitable for the identification of the above mentioned taxa. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Cistanche species. Additionally, the average genetic distance of psbA-trnH ranging from 0.077% to 0.743%. In contrast, the intra-specific variation among Cistanche species was found to be significantly different from those of other species, with percentages of variation studied ranged from 0% to 0.007%. The sequence difference between the psbA-trnH sequences of Cistanche species and Orobanche pycnostachya ranged from 0.979% to 1.149%. The distance between the Cistanche species and Boschniakia rossica ranged from 1.066% to 1.224%. Our results suggest that the psbA-trnH intergenic spacer region represent a barcode that can be used to identify Cistanche species and other morphologically undistinguishable species.

Complete pathway elucidation of echinacoside in Cistanche tubulosa and de novo biosynthesis of phenylethanoid glycosides

Echinacoside (ECH), one of the most representative phenylethanoid glycosides (PhGs), has considerable neuroprotective effects and is an effective ingredient in numerous commercial drugs. Here, we elucidate the complete ECH biosynthetic pathway in the medicinal plant Cistanche tubulosa. In total, 14 related genes are cloned and functionally characterized. Two upstream pathways for tyrosol biosynthesis from L-tyrosine are identified: one includes separate decarboxylation, deamination and reduction steps; the other uses microbial-like transamination, decarboxylation and reduction steps. In addition, a distinct downstream assembly process from tyrosol to ECH is revealed that includes sequential glucosylation, acylation, hydroxylation, and rhamnosylation to form acteoside, and ends with a final glucosylation converting acteoside to ECH. Furthermore, the de novo synthesis of 23 PhG derivatives is achieved via the heterologous expression of different combinations of the functional genes in tobacco. Our findings provide insights into the biosynthesis of ECH and a platform for alternative production of complex PhGs.

[Study on identification of cistanche hebra and its adulterants by PCR amplification of specific alleles based on ITS sequences]

To explore the new method of discriminating Cistanche deserticola, Cynomorium songaricum and Orobanche pycnostachya by using PCR amplification of specific alleles. 30 samples of the different C. deserticola, 21 samples of C. songaricum and O. pycnostachya were collected. The total DNA of the samples were extracted, the ITS sequences from C. deserticola, C. songaricum and O. pycnostachya were amplified by PCR and sequenced unidirectionally. These sequences were aligned by using ClustulW. Specific primer was designed according to the ITS sequences of specific alleles, and PCR reaction system was optimized. Additionally, compare with the identification of specific PCR method and DNA sequence analysis method. The result showed that the 331 bp identification band for C. deserticola and the adulterants not amplified bands by a single PCR reaction, which showed good identification ability to the three species. PCR amplification of specific alleles can be used to identify C. deserticola, C. songaricum and O. pycnostachya successfully.