scholarly journals Development of Plastid Genomic Resources for Discrimination and Classification of Epimedium wushanense (Berberidaceae)

2019 ◽  
Vol 20 (16) ◽  
pp. 4003 ◽  
Author(s):  
Guo ◽  
Ren ◽  
Xu ◽  
Liao ◽  
Song ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Trees ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Important Species ◽  
Plastid Genomes ◽  
First Time

Epimedium wushanense (Berberidaceae) is recorded as the source plant of Epimedii Wushanensis Folium in the Chinese Pharmacopoeia. However, controversies exist on the classification of E. wushanense and its closely related species, namely, E. pseudowushanense, E. chlorandrum, E. mikinorii, E. ilicifolium, and E. borealiguizhouense. These species are often confused with one another because of their highly similar morphological characteristics. This confusion leads to misuse in the medicinal market threatening efficiency and safety. Here, we studied the plastid genomes of these Epimedium species. Results show that the plastid genomes of E. wushanense and its relative species are typical circular tetramerous structure, with lengths of 156,855–158,251 bp. A total of 112 genes were identified from the Epimedium plastid genomes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. A loss of rpl32 gene in E. chlorandrum was found for the first time in this study. The phylogenetic trees constructed indicated that E. wushanense can be distinguished from its closely related species. E. wushanense shows a closer relationship to species in ser. Dolichocerae. In conclusion, the use of plastid genomes contributes useful genetic information for identifying medicinally important species E. wushanense and provides new evidence for understanding phylogenetic relationships within the Epimedium genus.

scholarly journals Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

2018 ◽  
Vol 123 (5) ◽  
pp. 857-865 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Ovidiu Paun ◽  
Mark W Chase ◽  
Peter S Ashton ◽  
A S Kamariah ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Plastid Genomes ◽  
Snp Data ◽  
Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

scholarly journals Comparative analysis of the complete chloroplast genome sequences of six species of Pulsatilla Miller, Ranunculaceae

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Tingting Zhang ◽  
Yanping Xing ◽  
Liang Xu ◽  
Guihua Bao ◽  
Zhilai Zhan ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Trees ◽  
Single Copy ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Closely Related Species ◽  
Protein Coding ◽  
Simple Sequence Repeat Analysis ◽  
Chloroplast Genomes ◽  
Cp Genome

Abstract Background Baitouweng is a traditional Chinese medicine with a long history of different applications. Although referred to as a single medicine, Baitouweng is actually comprised of many closely related species. It is therefore critically important to identify the different species that are utilized in these medicinal applications. Knowledge about their phylogenetic relationships can be derived from their chloroplast genomes and may provide additional insights into development of molecular markers. Methods Genomic DNA was extracted from six species of Pulsatilla and then sequenced on an Illumina HiSeq 4000. Sequences were assembled into contigs by SOAPdenovo 2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the cp genomes of the six species were analyzed and compared with closely related species. Additionally, phylogenetic trees were constructed, based on single nucleotide polymorphisms (SNPs) and 51 shared protein-coding gene sequences in the cp genome among all 31 species via maximum likelihood. Results The size of cp genomes of P. chinensis (Bge.) Regel, P. chinensis (Bge.) Regel var. kissii (Mandl) S. H. Li et Y. H. Huang, P. cernua (Thunb.) Bercht. et Opiz f. plumbea J. X. Ji et Y. T. zhao, P. dahurica (Fisch.) Spreng, P. turczaninovii Kryl. et Serg, and P. cernua (Thunb.) Bercht. et Opiz. were 163,851 bp, 163,756 bp, 162,481 bp, 162,450 bp, 162,795 bp, and 162,924 bp, respectively. Each species included two inverted repeat regions, a small single-copy region, and a large single-copy region. A total of 134 genes were annotated, including 90 protein-coding genes, 36 tRNAs, and eight rRNAs across all species. In simple sequence repeat analysis, only P. dahurica was found to contain hexanucleotide repeats. A total of 26, 39, 32, 37, 32 and 43 large repeat sequences were identified in the genic regions of the six Pulsatilla species. Nucleotide diversity analysis revealed that the rpl36 gene and ccsA-ndhD region have the highest Pi value. In addition, two phylogenetic trees of the cp genomes were constructed, which laced all Pulsatilla species into one branch within Ranunculaceae. Conclusions We identified and analyzed the cp genome features of six species of P. Miller, with implications for species identification and phylogenetic analysis.

scholarly journals Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes

2020 ◽  
Author(s):  
Joonhyung Jung ◽  
Changkyun Kim ◽  
Joo-Hwan Kim
Keyword(s):  
Chloroplast Genome ◽  
Structural Variations ◽  
Protein Coding ◽  
Morphological Variations ◽  
Genome Data ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Recent Classification ◽  
First Time

Abstract BackgroundCommelinaceae (Commelinales) comprise 41 genera and widely distributed in both the Old and New Worlds except Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Nowadays, many researchers are commonly using complete chloroplast genome data for inferring evolution of land plants. In this study, we completed 15 new chloroplast genome sequences of subfamily Commelinoideae using Mi-seq platform. We utilized genome data for the first time to reveal the structural variations and reconstruct the problematic positions of genera.Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15) and former two genes might be a synapomorphy within the Commelinales. Only four species in tribe Commelineae appear IR expansion which affected duplication of rpl22 gene. We identified inversions which range from approximately 3 to 15 kb from four taxa (Murdannia, Streptolirion, Amischotolype, and Belosynapsis). The phylogenetic analyse using 77 chloroplast protein coding genes with maximum parsimony, maximum likelihood, and the Bayesian inference suggest that Palisota connected with tribe Commelineae with high support values, differ from recent classification of Commelinaceae. Also, we resolved unclear position of Streptoliriinae and monophyly of Dichorisandrinae.Conclusions In this study, we provide detailed information of the 15 plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used for inferring evolutionary history about this family. Also, we need a further research to revise position of Palisota in recent classification.

scholarly journals Complete Mitochondrial Genome Sequence of Bos Frontalis (Gayal) of Bangladesh

2021 ◽  
Author(s):  
Gautam Kumar Deb ◽  
Razia Khatun ◽  
Shakh Mohammed Jahangir Hossain ◽  
Shamsur Rahaman ◽  
Md. Anamul Bahar Bhuiyan ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Related Species ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Gene Arrangement ◽  
Trna Genes ◽  
Closely Related Species ◽  
Protein Coding ◽  
Protein Coding Genes

Abstract Background: Complete mitochondrial genome of Bos frontalis will aid in the investigation of evolutionary links between closely related species. Bos frontalis mitogenome contains 37 genes and a control region. We discover the first complete mitogenome of Bos frontalis found in Bangladesh which was obtained from whole-genome sequencing of Bos frontalis.Results: Bos frontalis mitogenome is 16,347 bp long, with an AT-based nucleotide composition (60.21%). It contains 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region (D-loop). This circular genome starts with ND6(negative strand) and ends at ND5(positive strand). Protein coding genes lost 24 bases and tRNA genes gained 27 bases compared to closely related species. Phylogenetic analysis of the mitochondrial genome of 26 closely related species from 8 congeneric species was conducted by the maximum likelihood method with 1000 bootstrap iteration.Conclusion: Our studied Bos frontalis mitochondrial genome has a similar gene arrangement compared with other Bos species. It has almost the same amount of AT and GC content, but notably the ND6 gene lacks AT skew and GC skew than that of the other two comparing species. PCG’s loss in size might be a continuous process of evolution. The mitochondrial genome is regarded as a critical tool for species identification and monitoring populations of conservation concern.

The Complete Chloroplast Genome of Chinese Hickory (Carya Cathayensis) and Genetic Comparison to Its Closely Related Species

2021 ◽  
Author(s):  
Xiangtao Zhu ◽  
Jianshuang Shen ◽  
Xueqin Li ◽  
Xia Chen ◽  
Xiaoling Huang ◽  
...  
Keyword(s):  
Related Species ◽  
Eastern China ◽  
Gc Content ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Closely Related Species ◽  
Important Species ◽  
Carya Cathayensis ◽  
Cp Genome

Abstract Background: Carya cathayensis, an important economic nut tree, is narrowly endemic to Eastern China in the wild. Although the nuclear genome of this plant has been reported recently, its chloroplast (cp) genome is yet to be decrypted. Results: Here, the complete cp genome of C. cathayensis was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%. It displays a quadripartite structure with a large single copy (LSC) region of 90,127 bp and a small single copy (SSC) region of 18,760 bp, separated by a pair of inverted repeats (IRs) of 25,969 bp. The genome contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The codon usage frequency and repeat sequences (including 252 simple sequence repeats (SSRs) and 55 long-repeats were identified. Conclusions: Phylogenetic analysis revealed that Juglandaceae is monophyletic, and that C. cathayensis is sister to C. kweichowensis and C. sinensis. Comparison of the C. cathayensis cp genome with those of the closely related species in Juglandaceae revealed that the noncoding regions are highly mutated, suggesting a great potential in phylogenetic researches. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.

scholarly journals Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

2020 ◽  
Author(s):  
Jingling Li ◽  
Jianmin Tang ◽  
Siyuan Zeng ◽  
Fang Han ◽  
Jing Yuan ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Interspecific Diversity

Abstract Background Pilea is a genus of perennial herbs from the family Urticaceae, which are used for courtyard ornamental. For some species, they are used as medicinal plants in traditional Chinese medicine as well. The morphological characteristics of medicinal species from Pilea are similar, and it is difficult to accurately distinguish them based only on morphological characteristics. Besides, the species classification of Pilea are still controversial. The classification of many species are still in an unresolved state. At present, there is no information about the chloroplast genomes of Pilea, which limits our further understanding of this genus. Here, we first reported 4 chloroplast genomes of Pilea taxa (P. mollis, P. glauca, P. peperomioides and P. serpyllacea), and performed comprehensive comparative analysis. Results The four chloroplast genomes have similar structural characteristics and gene order with other angiosperms. These genomes all have a typical quartile structure, which contains 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Besides, we detected SSRs and repeat sequences, and analyzed the expansion/contraction of IR regions. In particular, the comparative analysis showed a rather level of sequence divergence in the non-coding regions, even in the protein-coding regions of the four genome sequences, suggesting a high level of genetic diversity in Pilea. Moreover, we identified eight hypervariable regions, including petN-psbM; psbZ-trnG-GCC; trnT-UGU-trnL-UAA; accD-psbI; ndhF-rpl32; rpl32-trnL-UAG; ndhA-intron and ycf1, are proposed for use as DNA barcode regions. Phylogenetic analysis showed that four Pilea species form a monophyletic cluster with a 100% bootstrap value. Conclusion The results obtained here could provide abundant information for the phylogenetic position of Pilea and further species identification. High levels of sequences divergence promote our understanding of the interspecific diversity of this genus, also provide reference for the rational classification of unsolved species in the future.

scholarly journals Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joonhyung Jung ◽  
Changkyun Kim ◽  
Joo-Hwan Kim
Keyword(s):  
Nucleotide Diversity ◽  
Structural Variations ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Protein ◽  
Genome Data ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Current Classification

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

scholarly journals Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Congzhao Fan ◽  
Xiaojin Li ◽  
Jun Zhu ◽  
Jingyuan Song ◽  
Hui Yao
Keyword(s):  
Medicinal Plant ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its2 Sequence ◽  
Sequence Length ◽  
Local Alignment ◽  
Accurate Identification ◽  
Distance Method ◽  
Closely Related Species

The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

Six new species of Tonsilla Wang & Yin, 1992 (Araneae: Agelenidae) from southern China, with the first description of the male of T. yanlingensis (Zhang, Yin & Kim, 2000)

Zootaxa ◽  
2022 ◽  
Vol 5091 (2) ◽  
pp. 357-372
Author(s):  
MENG ZHANG ◽  
MUHAMMAD IRFAN ◽  
LU-YU WANG ◽  
ZHI-SHENG ZHANG
Keyword(s):  
New Species ◽  
Related Species ◽  
Southern China ◽  
New Combination ◽  
Distribution Map ◽  
Closely Related Species ◽  
First Time

Six new species of the spider genus Tonsilla Wang & Yin, 1992 are described from southern China: T. jinyunensis sp. nov. (♂♀) from Chongqing, T. jiugongensis sp. nov. (♂♀) from Hubei, T. subtruculenta sp. nov. (♂♀), T. rutunda sp. nov. (♂♀) and T. yueliangensis sp. nov. (♂) from Guizhou and T. subrostrum sp. nov. (♂♀) from Hunan. In addition, T. yanlingensis (Zhang, Yin & Kim, 2000) is redescribed and its male is described here for the first time. Tonsilla subyanlingensis Liu & Xu, 2020 is transferred to Draconarius Ovtchinnikov, 1999, hence the new combination Draconarius subyanlingensis (Liu & Xu, 2020) comb. nov. is established. The female of T. subyanlingensis Liu & Xu, 2020 should be treated as T. yanlingensis (Zhang, Yin & Kim, 2000). Detailed descriptions, photographs of copulatory organs and somatic features, a distribution map and comparisons with closely related species are presented.  

scholarly journals High Genetic Differentiation among European White Oak Species (Quercus spp.) at a Dehydrin Gene

2015 ◽  
Vol 43 (2) ◽  
pp. 582-588 ◽  
Author(s):  
Iacob CRĂCIUNESC ◽  
Barbara VORNAM ◽  
Ludger LEINEMANN ◽  
Reiner FINKELDEY ◽  
Neculae ȘOFLETEA ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Related Species ◽  
Population Level ◽  
Quercus Petraea ◽  
White Oak ◽  
Closely Related Species ◽  
Significant Differentiation ◽  
Dehydrin Gene ◽  
First Time ◽  
Two Populations

Dehydryn genes are involved in plant response to environmental stress and may be useful to examine functional diversity in relation to adaptive variation. Recently, a dehydrin gene (DHN3) was isolated in Quercus petraea and showed little differentiation between populations of the same species in an altitudinal transect. In the present study, inter- and intraspecific differentiation patterns in closely related and interfertile oaks were investigated for the first time at the DHN3 locus. A four-oak-species stand (Quercus frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L.) and two populations for each of five white oak species (Q. frainetto Ten., Q. petraea (Matt.) Liebl., Q. pubescens Willd., Q. robur L. and Q. pedunculiflora K. Koch) were analyzed. Three alleles shared by all five oak species were observed. However, only two alleles were present in each population, but with different frequencies according to the species. At population level, all interspecific pairs of populations showed significant differentiation, except for pure Q. robur and Q. pedunculiflora populations. In contrast, no significant differentiation (p > 0.05) was found among conspecific populations. The DHN3 locus proved to be very useful to differentiate Q. frainetto and Q. pubescens from Q. pedunculiflora (FST = 0.914 and 0.660, respectively) and Q. robur (FST = 0.858 and 0.633, respectively). As expected, the lowest level of differentiation was detected between the most closely related species, Q. robur and Q. pedunculiflora (FST = 0.020). Our results suggest that DHN3 can be an important genetic marker for differentiating among European white oak species.

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