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Wang JC, Chen HH, Hsu TW, Hung KH, Huang CC. A taxonomic revision of the genus Angelica (Apiaceae) in Taiwan with a new species A. aliensis. Bot Stud 2024; 65:3. [PMID: 38252347 PMCID: PMC10803708 DOI: 10.1186/s40529-023-00407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Angelica L. sensu lato is a taxonomically complex genus, and many studies have utilized morphological and molecular features to resolve its classification issues. In Taiwan, there are six taxa within Angelica, and their taxonomic treatments have been a subject of controversy. In this study, we conducted a comprehensive analysis incorporating morphological and molecular (cpDNA and nrDNA) characteristics to revise the taxonomic treatments of Angelica in Taiwan. RESULTS As a result of our research, we have revised the classification between A. dahurica var. formosana and A. pubescens and merged two varieties of A. morrisonicola into a single taxon. A new taxon, A. aliensis, has been identified and found to share a close relationship with A. tarokoensis. Based on the morphological and molecular characteristics data, it has been determined that the former three taxa should be grouped into the Eurasian Angelica clade, while the remaining four taxa should belong to the littoral Angelica clade. Furthermore, Angelica species in Taiwan distributed at higher altitudes displayed higher genetic diversity, implying that the central mountain range of Taiwan serves as a significant reservoir of plant biodiversity. Genetic drift, such as bottlenecks, has been identified as a potential factor leading to the fixation or reduction of genetic diversity of populations in most Angelica species. We provide key to taxa, synopsis, phenology, and distribution for each taxon of Taiwan. CONCLUSIONS Our comprehensive analysis of morphological and molecular features has shed light on the taxonomic complexities within Angelica in Taiwan, resolving taxonomic issues and providing valuable insights into the phylogenetic relationships of Angelica in Taiwan.
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Affiliation(s)
- Jenn-Che Wang
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Hung-Hsin Chen
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Tsai-Wen Hsu
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
- Forestry and Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Chi-Chun Huang
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan.
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2
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Wu CS, Sudianto E, Chiu HL, Chao CP, Chaw SM. Corrigendum: Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data. Front Plant Sci 2021; 12:771777. [PMID: 34659327 PMCID: PMC8519345 DOI: 10.3389/fpls.2021.771777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2021.713216.].
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Lung Chiu
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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3
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Paloi S, Mhuantong W, Luangsa-ard JJ, Kobmoo N. Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification of Cordyceps Species. J Fungi (Basel) 2021; 7:767. [PMID: 34575804 PMCID: PMC8467230 DOI: 10.3390/jof7090767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
While recent sequencing technologies (third generation sequencing) can successfully sequence all copies of nuclear ribosomal DNA (rDNA) markers present within a genome and offer insights into the intragenomic variation of these markers, high intragenomic variation can be a source of confusion for high-throughput species identification using such technologies. High-throughput (HT) amplicon sequencing via PacBio SEQUEL I was used to evaluate the intragenomic variation of the ITS region and D1-D2 LSU domains in nine Cordyceps species, and the accuracy of such technology to identify these species based on molecular phylogenies was also assessed. PacBio sequences within strains showed variable level of intragenomic variation among the studied Cordyceps species with C. blackwelliae showing greater variation than the others. Some variants from a mix of species clustered together outside their respective species of origin, indicative of intragenomic variation that escaped concerted evolution shared between species. Proper selection of consensus sequences from HT amplicon sequencing is a challenge for interpretation of correct species identification. PacBio consensus sequences with the highest number of reads represent the major variants within a genome and gave the best results in terms of species identification.
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Affiliation(s)
| | | | | | - Noppol Kobmoo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Development Agency (NSTDA), 113 Thailand Science Park, Phahonuyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand; (S.P.); (W.M.); (J.J.L.)
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4
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He J, Lyu R, Luo Y, Lin L, Yao M, Xiao J, Xie L, Wen J, Pei L, Yan S, Cheng J, Li J, Li L. An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene. Mol Phylogenet Evol 2021; 164:107259. [PMID: 34303792 DOI: 10.1016/j.ympev.2021.107259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
Abstract
Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas.
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Šlenker M, Kantor A, Marhold K, Schmickl R, Mandáková T, Lysak MA, Perný M, Caboňová M, Slovák M, Zozomová-Lihová J. Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides. Front Plant Sci 2021; 12:659275. [PMID: 33995457 PMCID: PMC8115912 DOI: 10.3389/fpls.2021.659275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/10/2021] [Indexed: 05/19/2023]
Abstract
Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid-nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian-Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.
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Affiliation(s)
- Marek Šlenker
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Kantor
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Karol Marhold
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Terezie Mandáková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin A. Lysak
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Michaela Caboňová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Judita Zozomová-Lihová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia
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Wu CS, Sudianto E, Chiu HL, Chao CP, Chaw SM. Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data. Front Plant Sci 2021; 12:713216. [PMID: 34456952 PMCID: PMC8385209 DOI: 10.3389/fpls.2021.713216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/16/2021] [Indexed: 05/10/2023]
Abstract
Bananas (Musa spp.) are some of the most important fruit crops in the world, contributing up to US$10 billion in export values annually. In this study, we use high-throughput sequencing to obtain genomic resources of high-copy DNA molecules in bananas. We sampled 13 wild species and eight cultivars that represent the three genera (Ensete, Musa, and Musella) of the banana family (Musaceae). Their plastomic, 45S rDNA, and mitochondrial scaffolds were recovered from genome skimming data. Two major clades (Clades I & II) within Musa are strongly supported by the three genomic compartment data. We document, for the first time, that the plastomes of Musaceae have expanded inverted repeats (IR) after they diverged from their two close relatives, Heliconiaceae (the lobster-claws) and Strelitziaceae (the traveler's bananas). The presence/absence of rps19 within IR regions reinforces the two intra-generic clades within Musa. Our comparisons of the bananas' plastomic and mitochondrial DNA sequence trees aid in identifying hybrid bananas' parentage. As the mitochondrial genes of Musa have elevated substitution rates, paternal inheritance likely plays an influential role on the Musa mitogenome evolution. We propose genome skimming as a useful method for reliable genealogy tracing and phylogenetics in bananas.
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Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hui-Lung Chiu
- Plant Germplasm Division, Taiwan Agricultural Research Institute, Taichung, Taiwan
| | | | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- *Correspondence: Shu-Miaw Chaw
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Jabeen S, Kiran M, Khan J, Ahmad I, Ahmad H, Sher H, Khalid AN. Amanitaahmadii, a new species of Amanita subgenus Amanitina section Validae from Pakistan. MycoKeys 2019; 56:81-99. [PMID: 31388329 PMCID: PMC6667395 DOI: 10.3897/mycokeys.56.31819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 12/26/2018] [Indexed: 01/12/2023] Open
Abstract
A new species from coniferous forests in Pakistan, Amanitaahmadii, is described on the basis of morpho-anatomy and molecular data set analyses. This species is characterized by its medium-sized to large basidiomata, grayish brown to brown pileal surface and rimose pileus margin with gray to dark brown verrucose veil remnants, a cream stipe with bulbous base having grayish brown or brown longitudinal striations above the annulus, a scaly surface towards the base, globose to broadly ellipsoid and amyloid basidiospores, and the absence of clamped septa in all tissues. Molecular phylogenetic analyses based on ITS and LSU sequences confirmed its identity as a new taxon nested within subgen. Amanitinasect.Validae.
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Affiliation(s)
- Sana Jabeen
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Punjab, Pakistan University of Education Lahore Pakistan.,Department of Botany, University of the Punjab, Quaid-e-Azam Campus-54590, Lahore, Punjab, Pakistan University of the Punjab Lahore Pakistan
| | - Munazza Kiran
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus-54590, Lahore, Punjab, Pakistan University of the Punjab Lahore Pakistan
| | - Junaid Khan
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan University of Swat Swat Pakistan
| | - Ishtiaq Ahmad
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Punjab, Pakistan University of Education Lahore Pakistan.,Centre of Plant Biodiversity and Conservation, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan Islamia College University Peshawar Pakistan.,Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan University of Peshawar Peshawar Pakistan
| | - Habib Ahmad
- Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan University of Peshawar Peshawar Pakistan
| | - Hassan Sher
- Center for Plant Sciences and Biodiversity, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan University of Swat Swat Pakistan
| | - Abdul Nasir Khalid
- Department of Botany, University of the Punjab, Quaid-e-Azam Campus-54590, Lahore, Punjab, Pakistan University of the Punjab Lahore Pakistan
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8
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Morales-Briones DF, Tank DC. Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. Am J Bot 2019; 106:415-437. [PMID: 30882906 DOI: 10.1002/ajb2.1253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed. METHODS Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group. KEY RESULTS We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae. CONCLUSIONS Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.
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Affiliation(s)
- Diego F Morales-Briones
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
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9
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Sun Y, Yang H, Zhang Q, Qin L, Li P, Lee J, Chen S, Rahman K, Kang T, Jia M. Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia. PeerJ 2019; 7:e6194. [PMID: 30648018 PMCID: PMC6330945 DOI: 10.7717/peerj.6194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/01/2018] [Indexed: 11/20/2022] Open
Abstract
Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
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Affiliation(s)
- Yiqi Sun
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Dalian, Liaoning, China
| | - Hong Yang
- School of Medicine, Tongji University, Shanghai, China
| | - Qiaoyan Zhang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Luping Qin
- Department of Pharmacognosy, Second Military Medical University School of Pharmacy, Shanghai, China.,College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Joongku Lee
- Department of Environment and Forest Resources, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, South Korea
| | - Shichao Chen
- College of Life Science and Technology, Tongji University, Shanghai, China
| | - Khalid Rahman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Tingguo Kang
- College of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, Dalian, Liaoning, China
| | - Min Jia
- Department of Pharmacognosy, Second Military Medical University School of Pharmacy, Shanghai, China
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Liu BB, Liu GN, Hong DY, Wen J. Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data. Front Plant Sci 2019; 10:1731. [PMID: 32117331 PMCID: PMC7019104 DOI: 10.3389/fpls.2019.01731] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/09/2019] [Indexed: 05/03/2023]
Abstract
The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya and Rhaphiolepis have been supported to form a clade, the monophyly of Eriobotrya and Rhaphiolepis at the genus level has never been well tested and their phylogenetic positions in Maleae still remain uncertain. This study aims to reconstruct a robust phylogeny of the ER clade in the framework of Maleae with a broad taxon sampling and clarify the phylogenetic relationship between Eriobotrya and Rhaphiolepis. This study employed sequences of the whole plastome (WP) and entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach and included 83 samples representing 76 species in 32 genera of Rosaceae, especially Maleae. The Maximum Likelihood (ML) and Bayesian Analysis (BI) based on three datasets, i.e., WP, coding sequences of plastome (CDS), and nrDNA, strongly supported the paraphyly of Eriobotrya, within which Rhaphiolepis was nested. Our plastid tree supported the sister relationship between the ER clade and Heteromeles, and the nrDNA tree, however, did not resolve the phylogenetic placement of the ER clade in Maleae. Strong incongruence between the plastid and the nuclear trees is most likely explained by hybridization events, which may have played an important role in the evolutionary history of the ER clade. Molecular, morphological, and geographic evidence all supports the merge of Eriobotrya with Rhaphiolepis, which has the nomenclatural priority. We herein transferred 36 taxa of Eriobotrya to Rhaphiolepis. We also proposed a new name, Rhaphiolepis loquata B.B.Liu & J.Wen, for the economically important loquat, as the specific epithet "japonica" was pre-occupied in Rhaphiolepis.
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Affiliation(s)
- Bin-Bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Guang-Ning Liu
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - De-Yuan Hong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- *Correspondence: Jun Wen,
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11
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Ali MA. Species-specific molecular signature of Commiphora species of Saudi Arabia inferred from internal transcribed spacer sequences of nuclear ribosomal DNA. Saudi J Biol Sci 2018; 25:1298-1301. [PMID: 30505173 PMCID: PMC6252017 DOI: 10.1016/j.sjbs.2018.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/29/2022] Open
Abstract
The deciduous habit and tendency to produce flowers prior to developing leaves, and a predominantly dioecious system of breeding in the genus Commiphora leads to difficulties in its taxonomic identification at species level. The characteristics of easy amplification by universal primer, shorter length and higher discrimination power at the species level makes the internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA (nrDNA) to a smart gene for generating species-specific phylogenetic inferences in most of the plants groups. The present study deals the ITS sequence of nrDNA based molecular genotyping of seven species of the genus Commiphora of Saudi Arabia. The molecular phylogenetic analysis of ITS sequences of nrDNA of Commiphora species distributed in Saudi Arabia reveals the the occurrence of C. madagascariens in Saudi Arabia.
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12
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Ajmal Ali M. Molecular authentication of Anthemis deserti Boiss. (Asteraceae) based on ITS2 region of nrDNA gene sequence. Saudi J Biol Sci 2019; 26:155-9. [PMID: 30622420 DOI: 10.1016/j.sjbs.2018.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 11/05/2022] Open
Abstract
The dried plant material of medicinally important Anthemis deserti Boiss. (family: Asteraceae) especially when it remains in the powdered form often look similar to Anthemis melampodina Del.; and therefore, difficult to distinguish, finally lead to chances of adulteration. The adulteration in medicinal plants effects on the efficacy of the drugs. The molecular authentication of herbal plant materials such as based on the internal transcribed spacer 2 (ITS2) sequences of nuclear ribosomal DNA (nrDNA) is considered as more reliable method compared to other the biochemical or histological methods. The present study aims to molecular authentication ofA. deserti based on molecular phylogenetic analyses of ITS2 gene sequence of nrDNA region. The ITS2 region of nrDNA of A. deserti were sequenced, and the molecular phylogenetic analyses were performed together with the GenBank sequences. The Maximum Parsimony tree revealed the close relationships of A. deserti with A. melampodina; however, the Neighbor-Joining and Maximum Likelihood tree clearly revealed that A. deserti is distinct from A. melampodina, which is also supported by the differences in nucleotides at five diffident positions (i.e. 22, 28, 87, 175 and 198) in the DNA sequence alignment.
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Chattopadhyay P, Banerjee G, Banerjee N. Distinguishing Orchid Species by DNA Barcoding: Increasing the Resolution of Population Studies in Plant Biology. OMICS 2018; 21:711-720. [PMID: 29257732 DOI: 10.1089/omi.2017.0131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]. To solve this challenge, we have screened the four well-established candidate gene sequences (i.e., rbcL, matK, trnL-trnF IGS, and 18S-ITS1-5.8S-ITS2-28S nrDNA) of 65 Indian orchid species. We also have included 31 different species of Dendrobium to identify the suitable locus for resolving the phylogeny-related problem below the taxonomic rank of genus. The Consortium for the Barcode of Life has recommended the locus rbcL and matK for barcoding of all land plants, including orchids. However, in this study, matK and rbcL (species resolving capacity 52% and 48%, respectively) were found to work above the taxonomic limit of genus, and thus cannot be considered a suitable tool to resolve closely related species of Dendrobium, whereas, we found that the locus 18S-ITS1-5.8S-ITS2-28S nrDNA is the best choice with the highest species resolving ability (95.23%) and the highest mean Kimura 2-parameter distance (254 for intergeneric and 144 for intrageneric) for phylogeny construction, and thus have been taken as the most promising single-locus barcode for orchids.
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Affiliation(s)
- Pritam Chattopadhyay
- 1 Department of Botany, Visva-Bharati , Santiniketan, India .,2 Department of Biotechnology, Gauhati University , Guwahati, India
| | - Goutam Banerjee
- 3 Department of Biochemistry, University of Calcutta , Kolkata, India
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Arshed MJC, Valdez MB, Alejandro GJD. Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack ( Lasiantheae: Rubiaceae). Pharmacogn Mag 2017; 13:553-558. [PMID: 29200712 PMCID: PMC5701390 DOI: 10.4103/pm.pm_1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/01/2017] [Indexed: 11/04/2022] Open
Abstract
Introduction The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation. Materials and Methods In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers (matK, rbcL, rps16, and trnT-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species. Results The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, matK and rbcL are recommended but with minimal resolution of species. While trnT-F showed moderate interspecific variations and resolution of Lasianthus species, rps16 has the lowest interspecific divergence and resolution of species. Conclusion Consequently, ITS is the potential ideal DNA barcode for Lasianthus species. SUMMARY ITS, matK, and rps16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by matK, rbcL, trnT-F, and rps16, respectivelyAll markers except rps16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, matK: maturase K, rbcL: ribulose-1,5-biphospahte-carboxylase, rps16: ribosomal protein 16 small subunit gene.
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Affiliation(s)
| | - Marcos B Valdez
- Department of Biological Sciences, Institute of Arts and Sciences, Far Eastern University, Nicanor Reyes Street, Sampaloc, 1008 Manila, Philippines
| | - Grecebio Jonathan D Alejandro
- The Graduate School and Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd, 1015 Manila, Philippines
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Chen CS, Huang CT, Hseu RS. Evidence for two types of nrDNA existing in Chinese medicinal fungus Ophiocordyceps sinensis. AIMS Genet 2017; 4:192-201. [PMID: 31435508 PMCID: PMC6690242 DOI: 10.3934/genet.2017.3.192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/25/2017] [Indexed: 11/18/2022]
Abstract
Nuclear ribosomal DNA (nrDNA) sequences are widely used in the molecular classification of fungi. Previous phylogenetic studies of highly-valued traditional Chinese medicinal fungus Ophiocordyceps sinensis were mostly based on 18S and internal transcribed spacer (ITS) regions (ITS1, 5.8S and ITS2) of nrDNA. However, the disparity manifest in the low sequences identities between different O. sinensis isolates has led to argumentative hypotheses for this phenomenon, such as the “species complex” or “cryptic species” hypotheses. In the present study, four types of nrDNA (GC, AT-1, AT-2, and T) were identified using four primer pairs to amplify the nrDNA of six O. sinensis isolates. We demonstrate that each O. sinensis isolate contained two types of nrDNA, the omnipresent GC-type and a coexistent type alternating between the remaining three. This crucial discovery challenges the established notion of one type of nrDNA per species. We therefore propose that the composition of nrDNA types should be taken into consideration in studies of fungal genetics and classification.
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Affiliation(s)
- Chih-Sheng Chen
- Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
| | - Ching-Tsan Huang
- Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
| | - Ruey-Shyang Hseu
- Institute of Microbiology and Biochemistry, College of Life Science, National Taiwan University, Taipei, Taiwan (R.O.C)
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Takano A. Taxonomic study on Japanese Salvia (Lamiaceae): Phylogenetic position of S. akiensis, and polyphyletic nature of S. lutescens var. intermedia. PhytoKeys 2017; 80:87-104. [PMID: 28781560 PMCID: PMC5543607 DOI: 10.3897/phytokeys.80.11611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Both Salvia akiensis and S. lutescens (Lamiaceae) are endemic to Japan. Salvia akiensis was recently described in 2014 in the Chugoku (= SW Honshu) region, and each four varieties of S. lutescens distributed allopatrically. Among varieties in S. lutescens, var. intermedia show a disjunctive distribution in the Kanto (=E Honshu) and Kinki (= W Honshu) regions. Recent field studies of S. lutescens var. intermedia revealed several morphological differences between the Kanto and Kinki populations. Here, I evaluated these differences among Salvia lutescens var. intermedia and its allies with morphological analysis and molecular phylogenetic analyses of nuclear ribosomal DNA (internal and external transcribed spacer regions) and plastid DNA (ycf1-rps15 spacer, rbcL, and trnL-F) sequences. Both morphological analysis and molecular phylogenetic analyses showed that S. lutescens var. intermedia from the Kinki region and var. lutescens were closely related to each other. However, var. intermedia from the Kanto region exhibited an association with S. lutescens var. crenata and var. stolonifera, which also grew in eastern Japan, rather than var. intermedia in the Kinki region. These results indicated that S. lutescens var. intermedia is not a taxon with a disjunctive distribution, but a combination of two or more allopatric taxa. Present study also suggested that S. akiensis was most closely related to S. omerocalyx.
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Affiliation(s)
- Atsuko Takano
- Division of Natural History, Museum of Nature and Human Activities, Hyogo. Yayoigaoka 6, Sanda, Hyogo 669-1546, Japan
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Sulzbacher MA, Grebenc T, García MÁ, Silva BD, Silveira A, Antoniolli ZI, Marinho P, Münzenberger B, Telleria MT, Baseia IG, Martín MP. Molecular and morphological analyses confirm Rhizopogon verii as a widely distributed ectomycorrhizal false truffle in Europe, and its presence in South America. Mycorrhiza 2016; 26:377-88. [PMID: 26763005 PMCID: PMC4909799 DOI: 10.1007/s00572-015-0678-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/28/2015] [Indexed: 05/28/2023]
Abstract
The genus Rhizopogon includes species with hypogeous or subepigeus habit, forming ectomycorrhizae with naturally occurring or planted pines (Pinaceae). Species of the genus Rhizopogon can be distinguished easily from the other hypogeous basidiomycetes by their lacunose gleba without columella and their smooth elliptical spores; however, the limit between species is not always easy to establish. Rhizopogon luteolus, the type species of the genus, has been considered one of the species that are more abundant in Europe, as well as it has been cited in pine plantation of North and South America, different parts of Africa, Australia, and New Zealand. However, in this study, based on molecular analyses of the ITS nuclear ribosomal DNA (nrDNA) sequences (19 new sequences; 37 sequences from GenBank/UNITE, including those from type specimens), we prove that many GenBank sequences under R. luteolus were misidentified and correspond to Rhizopogon verii, a species described from Tunisia. Also, we confirm that basidiomes and ectomycorrhizae recently collected in Germany under Pinus sylvestris, as well as specimens from South of Brazil under Pinus taeda belong to R. verii. Thanks to the numerous ectomycorrhizal tips collected in Germany, a complete description of R. verii/P. sylvestris ectomycorrhiza is provided. Moreover, since in this paper the presence of R. verii in South America is here reported for the first time, a short description of basidiomes collected in Brazil, compared with collections located in different European herbaria, is included.
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Affiliation(s)
- Marcelo A Sulzbacher
- Departamento de Micologia/CCB, Universidade Federal de Pernambuco, Av. Prof. Nelson Chaves, s/n, CEP: 50670-901, Recife, Pernambuco, Brazil
| | - Tine Grebenc
- Slovenian Forestry Institute Večna pot 2, SI-1000, Ljubljana, Slovenia
| | - Miguel Á García
- Department of Biology, University of Toronto, 3359 Mississagua Road, Mississagua, ON, L5L 1C6, Canada
| | - Bianca D Silva
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, CEP: 59072-970, Natal, Rio Grande do Norte, Brazil
| | - Andressa Silveira
- Departamento de Solos, Universidade Federal de Santa Maria, CCR, Campus Universitário, 971050-900, Santa Maria, Rio Grande do Sul, Brazil
| | - Zaida I Antoniolli
- Departamento de Solos, Universidade Federal de Santa Maria, CCR, Campus Universitário, 971050-900, Santa Maria, Rio Grande do Sul, Brazil
| | - Paulo Marinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, CEP: 59072-970, Natal, Rio Grande do Norte, Brazil
| | - Babette Münzenberger
- Institute for Landscape Biogeochemistry, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Straße 84, 15374, Müncheberg, Germany
| | - M Teresa Telleria
- Departamento de Micología, Real Jardín Botánico, RJB-CSIC, Plaza Murillo 2, Madrid, 28014, Spain
| | - Iuri G Baseia
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, CEP: 59072-970, Natal, Rio Grande do Norte, Brazil
| | - María P Martín
- Departamento de Micología, Real Jardín Botánico, RJB-CSIC, Plaza Murillo 2, Madrid, 28014, Spain.
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Chen T, Chen Q, Luo Y, Huang ZL, Zhang J, Tang HR, Pan DM, Wang XR. Phylogeography of Chinese cherry (Prunus pseudocerasus Lindl.) inferred from chloroplast and nuclear DNA: insights into evolutionary patterns and demographic history. Plant Biol (Stuttg) 2015; 17:787-97. [PMID: 25521479 DOI: 10.1111/plb.12294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 12/10/2014] [Indexed: 05/16/2023]
Abstract
Chinese cherry (Prunus pseudocerasus Lindl.) is a commercially valuable fruit crop in China. In order to obtain new insights into its evolutionary history and provide valuable recommendations for resource conservation, phylogeographic patterns of 26 natural populations (305 total individuals) from six geographic regions were analyzed using chloroplast and nuclear DNA fragments. Low levels of haplotype and nucleotide diversity were found in these populations, especially in landrace populations. It is likely that a combined effect of botanical characteristics impact the effective population size, such as inbreeding mating system, long life span, as well as vegetative reproduction. In addition, strong bottleneck effect caused by domestication, together with founder effect after dispersal and subsequent demographic expansion, might also accelerate the reduction of the genetic variation in landrace populations. Interestingly, populations from Longmen Mountain (LMM) and Daliangshan Mountain (DLSM) exhibited relatively higher levels of genetic diversity, inferring the two historical genetic diversity centers of the species. Moreover, moderate population subdivision was also detected by both chloroplast DNA (GST = 0.215; NST = 0.256) and nuclear DNA (GST = 0.146; NST = 0.342), respectively. We inferred that the episodes of efficient gene flow through seed dispersal, together with features of long generation cycle and inbreeding mating system, were likely the main contributors causing the observed phylogeographic patterns. Finally, factors that led to the present demographic patterns of populations from these regions and taxonomic varieties were also discussed.
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Affiliation(s)
- T Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Q Chen
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Y Luo
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - Z-L Huang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - J Zhang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
| | - H-R Tang
- College of Horticulture, Sichuan Agricultural University, Ya'an, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - D-M Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - X-R Wang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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Ramírez-López I, Villegas-Ríos M, Salas-Lizana R, Garibay-Orijel R, Alvarez-Manjarrez J. Thelephora versatilis and Thelephora pseudoversatilis: two new cryptic species with polymorphic basidiomes inhabiting tropical deciduous and sub-perennial forests of the Mexican Pacific coast. Mycologia 2014; 107:346-58. [PMID: 25550304 DOI: 10.3852/14-151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thelephora is a genus of ectomycorrhizal basidiomycetes with basidiomes of varied shape which has been poorly studied in tropical ecosystems. In this paper, we present Thelephora versatilis and Thelephora pseudoversatilis, two new species collected in the same localities of deciduous and sub-perennial tropical forests of Jalisco, Mexico. Basidiomes of both species are brownish gray to violet brown with clavarioid-mesopodal, sub-resupinate or completely resupinate growth forms. In turn, phylogenetic analyses using nrDNA ITS sequences showed that these species are not closed related, nevertheless they are part of a well-supported clade conformed by several species of Thelephora, Tomentella and some undescribed Thelephorales. Morphological segregation of these species was attained by analyzing spore and hyphae characters using a wide sample. Significant statistical differences between the new species were observed regarding spore size, spine size and context hyphae width. This work exemplifies the relevance of integrating both morphological and molecular data, as well of the use of an appropriate sample size in order to discriminate among morphological cryptic species.
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Affiliation(s)
- Itzel Ramírez-López
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Margarita Villegas-Ríos
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F.
| | - Rodolfo Salas-Lizana
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Julieta Alvarez-Manjarrez
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
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Oh E, Gryzenhout M, Wingfield BD, Wingfield MJ, Burgess TI. Surveys of soil and water reveal a goldmine of Phytophthora diversity in South African natural ecosystems. IMA Fungus 2013; 4:123-31. [PMID: 23898418 PMCID: PMC3719200 DOI: 10.5598/imafungus.2013.04.01.12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 05/30/2013] [Indexed: 11/25/2022] Open
Abstract
Phytophthora species are well-known as destructive plant pathogens, especially in natural ecosystems. It is ironic, therefore, how little is known regarding the Phytophthora diversity in South African natural woody ecosystems. In this study, Phytophthora species were isolated using standard baiting techniques from 182 soil and water samples and these were identified based on ITS and coxI sequence data. The 171 resulting Phytophthora isolates resided in 14 taxa including six known species (P. multivora, P. capensis, P. cryptogea, P. frigida, P. cinnamomi, P. cinnamomi var. parvispora), the known but as yet unnamed Phytophthora sp. PgChlamydo, P. sp. emzansi, and P. sp. Kununurra and five novel taxa referred to as P. sp. stellaris, P. sp. Umtamvuna P. sp. canthium, P. sp. xWS, P. sp. xHennops. Four of the new taxa were found exclusively in water and two of these are hybrids. The most commonly isolated species from soil was P. multivora, a species recently described from Western Australia. Phytophthora frigida was isolated for the first time from stream water. With the exception of P. cinnamomi, very little is known regarding the biology, epidemiology or origin of Phytophthora in South Africa.
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Affiliation(s)
- Eunsung Oh
- Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Current address: E-Planet Co. Ltd. 345-9 Gasandong Gumcheongu, 153-802, Seoul, Republic of Korea
| | - Marieka Gryzenhout
- Department of Plant Sciences, University of the Free State, Bloemfontein 9301, South Africa
| | - Brenda D. Wingfield
- Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Michael J. Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Treena I. Burgess
- Department of Genetics and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Center for Phytophthora Science and Management, Murdoch University, Perth, Australia, 6150
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Choudhary RK, Ajmal Ali M, Lee J. Studies on genetic diversity among populations of Persicaria barbata (L.) H. Hara from India based on internal transcribed spacer sequences of nuclear ribosomal DNA. Saudi J Biol Sci 2010; 18:123-7. [PMID: 23961114 DOI: 10.1016/j.sjbs.2010.12.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 01/24/2023] Open
Abstract
Internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 16 populations of Persicaria barbata (L.) H. Hara (Polygonaceae) belonging to five geographical locations of India (Arunachal Pradesh, Himachal Pradesh, Bihar, Karnataka and Andaman Island) was sequenced. Analysis of nucleotide sequences reveals polymorphism among the populations. UPGMA analysis conducted on the ITS datasets shows that the sampled populations of P. barbata are grouped according to their geographic locations and are supposed to be evolved under reproductive isolation which most probably are due to the long distance distribution and population fragmentation.
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Affiliation(s)
- R K Choudhary
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon 305-806, South Korea
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