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

Li, Ying; Zhou, Jianguo; Chen, Xinlian; Cui, Yingxian; Xu, Zhichao; Li, Yonghua; Song, Jingyuan; Duan, Baozhong; Yao, Hui

doi:10.1038/s41598-017-13401-4

Cited by 63 publications

(77 citation statements)

References 78 publications

(118 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recorded hosts for this species include Glyptostrobus pensilis, Hevea brasiliensis, Dimocarpus longan, Moraceae spp. Taxillus chinensis is wildly used in various traditional Chinese medicine prescriptions such as the treatment of rheumatism, threatened abortion, hypertension, angina pectoris, stroke, and arrhythmia for many years in China (Li et al 2017). To facilitate its genetic research and contribute to its utilization, here, we report and characterize the complete plastome of T. chinensis (GenBank accession number: MN080717, this study) based on Illumina paired-end sequencing data.…”

Section: Taxillus Chinensis; Chloroplast Genome; Phylogenetic Analysismentioning

confidence: 99%

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China

Liu

Zhang

Shi

2019

Mitochondrial DNA Part B

View full text Add to dashboard Cite

Taxillus chinensis (DC) Danser, which is a hemiparasitic shrub distributed in southern China and Southeast Asian countries, is wildly used in various traditional Chinese medicine prescriptions. In this study, the complete chloroplast genome of the T. chinensis was assembled from the whole genome Illumina sequencing data. The complete plastome is a typical quadripartite structure with a length of 121,305 bp, which contained two inverted repeats (IRs) of 22,460 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 70,295 bp and 6090 bp, respectively. The plastome contains 106 genes, comprising 66 protein-coding genes, 28 tRNA genes, eight rRNA genes, and four processed pseudogenes. The overall GC content of the plastome is 37.4%, which is unevenly distributed across the whole chloroplast genome. The phylogenetic analysis shows that T. chinensis was closely related to the congeneric species T. sutchuenensis.

show abstract

Section: Taxillus Chinensis; Chloroplast Genome; Phylogenetic Analysismentioning

confidence: 99%

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China

Liu

Zhang

Shi

2019

Mitochondrial DNA Part B

View full text Add to dashboard Cite

show abstract

“…To date, a total of 14 plastomes in Santalales (Additional file 1) have been published [16,17,19,[41][42][43][44]…”

Section: Plastome Assembly Annotation and Comparisonmentioning

confidence: 99%

“…Such variable reliance on photosynthesis exerts different intensities of selective pressures on plastomes [3,7]. As a result, plant parasites often possess plastomes with varying degrees of degeneration, ranging from partial or complete loss of plastid-encoded NAD(P)H-dehydrogenase (NDH) complex in hemiparasitic plants [7,10,[16][17][18][19] to the functional loss of many photosynthesisassociated and energy production genes [7,11,[20][21][22][23][24][25][26], or even the complete loss of plastomes [27] in holoparasitic plants.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the complete plastomes of two flowering epiparasites (Phacellaria glomerata and P. compressa, Santalaceae, Santalales): gene content, organization and plastome degradation

Guo

Liu

Wang

et al. 2019

Preprint

View full text Add to dashboard Cite

Backgrounds: The transition to a heterotrophic lifestyle triggers reductive evolution of plastid genome (plastome) in both photosynthetic and non–photosynthetic parasites. A plant parasite parasitizing another plant parasite is referred to as epiparasitism, which is extremely rare in angiosperms. In despite of the particularly special lifeform of epiparasitic plants, their plastomes have not been characterized to date. Sequending such plastomes may enable new insights into the evolutionary pathway of plastome degradation associated with parasitism. Results: In this study, we generated complete plastomes of Phacellaria compressa and P. glomerata (Santalaceae, Santalales) through Illumina shotgun sequencing. Plastome assembly and comparison indicated that plastomes of both species exhibit the quadripartite structure typical of angiosperms, and that they possess similar size, structure, gene content, and arrangement of genes to other hemiparasites in Santalales, especially to those hemiparasites in Santalaceae. The plastomes of P. compressa and P. glomerata were characterized by the functional loss of plastid–encoded NAD(P)H–dehydrogenase and infA genes, which strongly coincides with the general pattern of plastome degradation observed in Santalales hemiparasites. Conclusion: Our study demonstrates that the shift to epiparasitism and reduced vegetative bodies in P. compressa and P. glomerata do not appear to cause any unique plastome degradation compared with their closely related hemiparasites. The epiparasitic lifestyle or an endophytic growth form observed in these two epiparasites may have limited impact on the reductive modification of their plastomes.

show abstract

“…Reads were trimmed and those with >10% Ns or with >10% low quality (Q 5) bases were filtered using NGSQC-Toolkit v2.3.3 (Patel and Jain 2012). Cleaned reads were assembled against the plastome of Taxillus sutchuenensis (GenBank Accession number: NC_036307.1) (Li et al 2017) using MITO bim v1.8 (Hahn et al 2013). Each sample's depth is 40Â in this study.…”

mentioning

confidence: 99%

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China

Yuan

Wang

Chen

et al. 2018

Mitochondrial DNA Part B

View full text Add to dashboard Cite

Scurrula notothixoides (Loranthaceae) is a hemiparasitic shrub distributed in forest margins of Southeast Asian countries. Here, we report and characterize the complete plastid genome sequence of S. notothixoides in an effort to provide genomic resources useful for the phylogenetic studies for Santalales. The complete plastome is 123,810 bp in length and contains the typical structure and gene content of angiosperm plastomes, including two inverted repeat (IR) regions of 23,101 bp, a large single copy (LSC) region of 71,448 bp and a small single copy (SSC) region of 6160 bp. The plastome contains 88 genes, consisting of 61 unique protein-coding genes, 23 unique tRNA genes and four unique rRNA genes. The overall A/T content in the plastome of S. notothixoides is 62.7%. Phylogenetic analyses were performed using the entire plastome, including spacers, introns, etc. and we recovered that S. notothixoides and Taxillus sutchuenensis was closely related. The complete plastome sequence of S. notothixoides will provide a useful resource for the phylogenetic studies for Santalales. ARTICLE HISTORY

show abstract

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

Cited by 63 publications

References 78 publications

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China

Complete chloroplast genome sequence of Taxillus chinensis (Loranthaceae): a hemiparasitic shrub in South China

Characterization of the complete plastomes of two flowering epiparasites (Phacellaria glomerata and P. compressa, Santalaceae, Santalales): gene content, organization and plastome degradation

Complete chloroplast genome sequence of Scurrula notothixoides (Loranthaceae): a hemiparasitic shrub in South China

Contact Info

Product

Resources

About