Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

10.21203/rs.3.rs-60093/v5 ◽

2020 ◽

Author(s):

Gurusamy Raman ◽

KyuTae Park ◽

Joo Hwan Kim ◽

SeonJoo Park

Keyword(s):

Genome Sequence ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Rrna Genes ◽

Trna Genes ◽

Comparative Analyses ◽

Sister Clade ◽

Mutational Hotspots ◽

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

BMC Genomics ◽

10.1186/s12864-020-07219-0 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Gurusamy Raman ◽

Kyu Tae Park ◽

JooHwan Kim ◽

SeonJoo Park

Keyword(s):

Genome Sequence ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Rrna Genes ◽

Trna Genes ◽

Comparative Analyses ◽

Sister Clade ◽

Mutational Hotspots ◽

Abstract Background The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted. Results Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Π > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value. Conclusion The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

10.21203/rs.3.rs-60093/v2 ◽

2020 ◽

Author(s):

Gurusamy Raman ◽

KyuTae Park ◽

Joo Hwan Kim ◽

SeonJoo Park

Keyword(s):

Genome Sequence ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Rrna Genes ◽

Trna Genes ◽

Comparative Analyses ◽

Sister Clade ◽

Mutational Hotspots ◽

Abstract Background: The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.Results: Here, the complete chloroplast (cp) genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 base pairs (bp) in length, with a quadripartite circular structure. The cp genome contained 115 unique genes, including 80 PCGs, 31 tRNA genes, and 4 rRNA genes. Comparative analyses revealed that X. spinosum contains a large number of repeats (999 repeats) and 701 SSRs in its cp genome. Fourteen divergences (Pi > 0.03) were found in the intergenic spacer regions. Phylogenetic analyses revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and an early-diverging lineage of subtribe Ambrosiinae, although this finding was supported with a very weak bootstrap value.Conclusion: The identified hotspot regions could be used as molecular markers for resolving phylogenetic relationships and species identification in the genus Xanthium.

Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

10.21203/rs.3.rs-60093/v1 ◽

2020 ◽

Author(s):

Gurusamy Raman ◽

KyuTae Park ◽

Joo Hwan Kim ◽

SeonJoo Park

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Plant Evolution ◽

Rrna Genes ◽

Trna Genes ◽

Mutational Hotspots ◽

Intergenic Regions ◽

Chloroplast Genome Sequence ◽

Abstract Background: The invasive alien species, Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, there are no extensive molecular studies for this plant. Results: Here, the complete chloroplast genome sequence of X. spinosum was assembled and analyzed. The cp genome of X. spinosum was 152,422 bp and possessed quadripartite circular structure. The cp genome contained 115 unique genes, including 80 protein-coding genes, 31 tRNA genes and 4 rRNA genes. Comparative analysis revealed that X. spinosum encoded a higher number of repeats (999 repeats) and 701 SSRs in their cp genome. Also, fourteen divergences (Pi > 0.03) were found in the intergenic regions. The accD gene underwent positive selection within Heliantheae, which contributes to further investigation of the adaptive plant evolution in the ecosystem. Additionally, the phylogenetic analysis revealed that Parthenium is a sister clade to both Xanthium and Ambrosia and it is an early-diverging lineage of subtribe Ambrosiinae though it supports with very weak bootstrap value. Conclusion: The identified hotspot regions were thought to be useful molecular markers for resolving phylogenetic relationships and species validation of Xanthium.

Complete Chloroplast Genomes of Ampelopsis humulifolia and Ampelopsis japonica: Molecular Structure, Comparative Analysis, and Phylogenetic Analysis

Plants ◽

10.3390/plants8100410 ◽

2019 ◽

Vol 8 (10) ◽

pp. 410 ◽

Cited By ~ 9

Author(s):

Xiaolei Yu ◽

Wei Tan ◽

Huanyu Zhang ◽

Han Gao ◽

Wenxiu Wang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

Gc Content ◽

Rrna Genes ◽

Trna Genes ◽

Protein Z ◽

Marker Selection ◽

Chloroplast Genomes ◽

Potential Marker ◽

Ampelopsis humulifolia (A. humulifolia) and Ampelopsis japonica (A. japonica), which belong to the family Vitaceae, are valuably used as medicinal plants. The chloroplast (cp) genomes have been recognized as a convincing data for marker selection and phylogenetic studies. Therefore, in this study we reported the complete cp genome sequences of two Ampelopsis species. Results showed that the cp genomes of A. humulifolia and A. japonica were 161,724 and 161,430 bp in length, respectively, with 37.3% guanine-cytosine (GC) content. A total of 114 unique genes were identified in each cp genome, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. We determined 95 and 99 small sequence repeats (SSRs) in A. humulifolia and A. japonica, respectively. The location and distribution of long repeats in the two cp genomes were identified. A highly divergent region of psbZ (Photosystem II reaction center protein Z) -trnG (tRNA-Glycine) was found and could be treated as a potential marker for Vitaceae, and then the corresponding primers were designed. Additionally, phylogenetic analysis showed that Vitis was closer to Tetrastigma than Ampelopsis. In general, this study provides valuable genetic resources for DNA barcoding marker identification and phylogenetic analyses of Ampelopsis.

Correction to: Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

BMC Genomics ◽

10.1186/s12864-021-07392-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gurusamy Raman ◽

Kyu Tae Park ◽

Joo-Hwan Kim ◽

SeonJoo Park

Keyword(s):

Chloroplast Genome ◽

Genome Sequence ◽

Comparative Analyses ◽

Mutational Hotspots ◽

Chloroplast Genome Sequence

An amendment to this paper has been published and can be accessed via the original article.

Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Plants ◽

10.3390/plants8100386 ◽

2019 ◽

Vol 8 (10) ◽

pp. 386

Author(s):

Hengwu Ding ◽

Ran Zhu ◽

Jinxiu Dong ◽

De Bi ◽

Lan Jiang ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Higher Plants ◽

Phylogenetic Analyses ◽

Structural Evolution ◽

Taxonomic Revision ◽

Rrna Operon ◽

Rrna Genes ◽

23S Rrna ◽

Trna Genes ◽

Phylogenetic Implications

The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

Comparative analysis of four Zantedeschia chloroplast genomes: expansion and contraction of the IR region, phylogenetic analyses and SSR genetic diversity assessment

PeerJ ◽

10.7717/peerj.9132 ◽

2020 ◽

Vol 8 ◽

pp. e9132

Author(s):

Shuilian He ◽

Yang Yang ◽

Ziwei Li ◽

Xuejiao Wang ◽

Yanbing Guo ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analyses ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Herbaceous Perennials ◽

Coding Regions ◽

Chloroplast Genomes ◽

Diversity Assessment ◽

The horticulturally important genus Zantedeschia (Araceae) comprises eight species of herbaceous perennials. We sequenced, assembled and analyzed the chloroplast (cp) genomes of four species of Zantedeschia (Z. aethiopica, Z. odorata, Z. elliottiana, and Z. rehmannii) to investigate the structure of the cp genome in the genus. According to our results, the cp genome of Zantedeschia ranges in size from 169,065 bp (Z. aethiopica) to 175,906 bp (Z. elliottiana). We identified a total of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. Comparison of our results with cp genomes from other species in the Araceae suggests that the relatively large sizes of the Zantedeschia cp genomes may result from inverted repeats (IR) region expansion. The sampled Zantedeschia species formed a monophylogenetic clade in our phylogenetic analysis. Furthermore, the long single copy (LSC) and short single copy (SSC) regions in Zantedeschia are more divergent than the IR regions in the same genus, and non-coding regions showed generally higher divergence than coding regions. We identified a total of 410 cpSSR sites from the four Zantedeschia species studied. Genetic diversity analyses based on four polymorphic SSR markers from 134 cultivars of Zantedeschia suggested that high genetic diversity (I = 0.934; Ne = 2.371) is present in the Zantedeschia cultivars. High genetic polymorphism from the cpSSR region suggests that cpSSR could be an effective tool for genetic diversity assessment and identification of Zantedeschia varieties.

The mitochondrial genome ofAncylostoma tubaeformefrom cats in China

Journal of Helminthology ◽

10.1017/s0022149x17000116 ◽

2017 ◽

Vol 92 (1) ◽

pp. 22-33 ◽

Cited By ~ 4

Author(s):

X.L. Shi ◽

Y.Q. Fu ◽

A.Y. Abdullahi ◽

M.W. Wang ◽

F. Yang ◽

...

Keyword(s):

Genome Sequence ◽

Phylogenetic Analyses ◽

Rrna Genes ◽

Trna Genes ◽

Its1 Sequence ◽

Genome Database ◽

Protein Coding ◽

Protein Coding Genes ◽

Close Phylogenetic Relationship ◽

Mt Genome

AbstractAncylostoma tubaeformemay infect canids, felids and humans, and pose a potential risk to public health. Polymerase chain reaction (PCR) techniques were used to amplify the complete mitochondrial (mt) genome sequence ofA. tubaeformefrom cats and to analyse its sequence characteristics after molecular identification based on the internal transcribed spacer ITS1+ sequence. The results show that the complete mt genome sequence (GenBank accession number KY070315) ofA. tubaeformefrom cats was 13,730 bp in length, including 12 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, two non-coding regions and an AT-rich region. The nucleotide content of A and T was 77.93%, biased toward A and T. Twelve protein-coding genes used ATT, TTG and GTG as initiation codons, and TAA, TAG, TA and T as termination codons. The length of the 22 tRNA genes ranged from 52 to 62 bp, their predicted secondary structures were D loops and V loops. The lengths of the two rRNAs were 958 and 697 bp. Phylogenetic analyses showed thatA. tubaeformefrom cats was in the lineage ofAncylostoma, having a close phylogenetic relationship withA. caninum. This study reports for the first time the mt genome ofA. tubaeformefrom cats in China, which could enhance the mt genome database of Ancylostomatidae nematodes, and it offers the scientific basis for further studies in the genetic diversity of hookworms among different hosts.