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Zhang Z, Liu G, Li M. Incomplete lineage sorting and gene flow within Allium (Amayllidaceae). Mol Phylogenet Evol 2024; 195:108054. [PMID: 38471599 DOI: 10.1016/j.ympev.2024.108054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.
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Affiliation(s)
- ZengZhu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Gang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Minjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China.
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He XJ. Integrating high-volume molecular and morphological data into the evolutionary studies of Allium. PLANT DIVERSITY 2024; 46:1-2. [PMID: 38343593 PMCID: PMC10851282 DOI: 10.1016/j.pld.2023.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/11/2023] [Indexed: 10/28/2024]
Affiliation(s)
- Xing-Jin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
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Lee M, Lee HY, Kang JS, Lee H, Park KJ, Park JY, Yang TJ. Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA. PLoS One 2023; 18:e0294457. [PMID: 37983242 PMCID: PMC10659177 DOI: 10.1371/journal.pone.0294457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Allium ulleungense (AU) and A. microdictyon (AM) are valuable medicinal and edible vegetables, referred to as mountain garlic in Korea. The identification of AU, AM and a neighboring species A. ochotense (AO) is difficult because of their morphological similarities. We collected samples from three species and 46 cultivated collections to understand the genetic diversity of these valuable Allium species. Among them, we sequenced six collections, including three species and three cultivating collections to obtain data from the plastid genome (plastome) and nuclear 45S ribosomal DNA (nrDNA) for super-barcoding. The AM and AO showed around 60 single nucleotide polymorphisms (SNPs) and 39 Insertion/Deletion (InDels) in the plastome but no variations in the nrDNA sequences. Conversely, the AU and AM showed more than 170 SNPs and 80 InDels in the plastomes, and 20 SNPs and 1 InDel were found in the 45S nrDNA sequences. Among the three cultivating collections, one TB collection was determined to be the AU type in both plastome and nrDNA sequences. However, the other two collections, JB and SA, showed the AM type plastome but were heterozygous in the 45S nrDNA sequences, indicating both AU and AM types (putative AM x AU hybrid). Ten molecular markers were developed based on sequence variations to identify these three species and assess their genetic diversity. A total of 49 collections were genotyped using the ten developed markers and classified into five groups: 14 AU, 22 AM, 1 AO, 3 putative AM x AU hybrids, and 9 putative AU x AM hybrid collections. Super-barcoding with plastomes and nrDNAs revealed the genetic diversity of the three Allium species and putative hybrids between species. The newly developed markers will facilitate species and hybrid identification, thereby benefiting marker-assisted molecular breeding of Allium species.
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Affiliation(s)
- Minyoung Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyo Young Lee
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyeji Lee
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Ki-Jin Park
- Gangwondo State Agricultural Research & Extension Services, Wild Vegetable Research Institute, Pyeongchang-gun, Gangwon State, Republic of Korea
| | - Jee Young Park
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Plant Genomics & Breeding Institute, Research Institute of Agriculture and Life Science, Forestry and Bioresources, College of Agriculture & Life Sciences, Seoul National University, Seoul, Republic of Korea
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Bhowmick BK, Sarkar S, Roychowdhury D, Patil SD, Lekhak MM, Ohri D, Rama Rao S, Yadav SR, Verma RC, Dhar MK, Raina SN, Jha S. Allium cytogenetics: a critical review on the Indian taxa. COMPARATIVE CYTOGENETICS 2023; 17:129-156. [PMID: 37304149 PMCID: PMC10252142 DOI: 10.3897/compcytogen.17.98903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 06/13/2023]
Abstract
The genus Allium Linnaeus, 1753 (tribe Allieae) contains about 800 species worldwide of which almost 38 species are reported in India, including the globally important crops (onion, garlic, leek, shallot) and many wild species. A satisfactory chromosomal catalogue of Allium species is missing which has been considered in the review for the species occurring in India. The most prominent base number is x=8, with few records of x=7, 10, 11. The genome size has sufficient clues for divergence, ranging from 7.8 pg/1C to 30.0 pg/1C in diploid and 15.16 pg/1C to 41.78 pg/1C in polyploid species. Although the karyotypes are seemingly dominated by metacentrics, substantial variation in nucleolus organizing regions (NORs) is noteworthy. The chromosomal rearrangement between A.cepa Linnaeus, 1753 and its allied species has paved way to appreciate genomic evolution within Allium. The presence of a unique telomere sequence and its conservation in Allium sets this genus apart from all other Amaryllids and supports monophyletic origin. Any cytogenetic investigation regarding NOR variability, telomere sequence and genome size in the Indian species becomes the most promising field to decipher chromosome evolution against the background of species diversity and evolution, especially in the Indian subcontinent.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata- 700006, West Bengal, IndiaDepartment of Botany, Scottish Church CollegeKolkataIndia
| | - Sayantika Sarkar
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
| | - Dipasree Roychowdhury
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
| | - Sayali D. Patil
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - Manoj M. Lekhak
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - Deepak Ohri
- Amity Institute of Biotechnology, Research Cell, Amity University Uttar Pradesh, Lucknow Campus, Lucknow- 226028, Uttar Pradesh, IndiaAmity University Uttar PradeshLucknowIndia
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya- 793022, IndiaNorth-Eastern Hill UniversityShillongIndia
| | - S. R. Yadav
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - R. C. Verma
- School of Studies in Botany, Vikram University, Ujjain, Madhya Pradesh 456010, IndiaVikram UniversityUjjainIndia
| | - Manoj K. Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir- 180006, IndiaUniversity of JammuJammuIndia
| | - S. N. Raina
- Amity Institute of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh- 201313, IndiaAmity UniversityNoidaIndia
| | - Sumita Jha
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
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Yang J, Kim SH, Gil HY, Choi HJ, Kim SC. New insights into the phylogenetic relationships among wild onions ( Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1124277. [PMID: 37025138 PMCID: PMC10070991 DOI: 10.3389/fpls.2023.1124277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
The genus Allium, with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within Allium have long been not resolved. Based on 76 species of Allium (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera Anguinum and Rhizirideum. We retrieved the three major evolutionary lines within Allium and found that the two subgenera Anguinum and Rhizirideum are monophyletic whereas others are highly polyphyletic (e.g., Allium, Cepa, Polyprason, and Melanocrommyum). Within the subgenus Anguinum, two strongly supported sublineages in East Asian and Eurasian-American were found. Allium tricoccum in North America belonged to the Eurasian clade. The distinct taxonomic status of A. ulleungense and its sister taxon were further determined. In subg. Rhizirideum, the Ulleung Island endemic A. dumebuchum shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic A. minus. Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian A. macrostemon (subg. Allium) and sister relationship between A. condensatum and A. chinense was suggested.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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Fu X, Xie DF, Zhou YY, Cheng RY, Zhang XY, Zhou SD, He XJ. Phylogeny and adaptive evolution of subgenus Rhizirideum (Amaryllidaceae, Allium) based on plastid genomes. BMC PLANT BIOLOGY 2023; 23:70. [PMID: 36726056 PMCID: PMC9890777 DOI: 10.1186/s12870-022-03993-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/09/2022] [Indexed: 06/01/2023]
Abstract
The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A. sect. Tenuissima, A. sect. Rhizirideum, A. sect. Eduardia, and A. sect. Caespitosoprason), A. sect. Caespitosoprason being merged into A. sect. Rhizomatosa recently. Previous studies on this subgenus mainly focused on separate sections. To investigate the inter-section and inter-subgenera phylogenetic relationships and adaptive evolution of A. subg. Rhizirideum, we selected thirteen representative species, which cover five sections of this subgenus and can represent four typical phenotypes of it. We conducted the comparative plastome analysis with our thirteen plastomes. And phylogenetic inferences with CDSs and complete sequences of plastomes of our thirteen species and another fifty-four related species were also performed. As a result, the A. subg. Rhizirideum plastomes were relatively conservative in structure, IR/SC borders, codon usage, and repeat sequence. In phylogenetic results, the inter-subgenera relationships among A. subg. Rhizirideum and other genus Allium subgenera were generally similar to the previous reports. In contrast, the inter-section relationships within our subgenus A. subg. Rhizirideum were newly resolved in this study. A. sect. Rhizomatosa and A. sect. Tenuissima were sister branches, which were then clustered with A. sect. Rhizirideum and A. sect. Eduardia successively. However, Allium Polyrhizum Turcz. ex Regel, type species of A. sect. Caespitosoprason, was resolved as the basal taxon of A. subg. Rhizirideum. Allium siphonanthum J. M. Xu was also found in clade A. subg. Cyathophora instead of clade A. subg. Rhizirideum. The selective pressure analysis was also conducted, and most protein-coding genes were under purifying selection. At the same time, just one gene, ycf2, was found under positive selection, and another three genes (rbcL, ycf1a, ycf1b) presented relaxed selection, which were all involved in the photosynthesis. The low temperature, dry climate, and high altitude of the extreme habitats where A. subg. Rhizirideum species grow might impose intense natural selection forces on their plastome genes for photosynthesis. In summary, our research provides new insights into the phylogeny and adaptive evolution of A. subg. Rhizirideum. Moreover, we suggest that the positions of the A. subg. Rhizirideum species A. polyrhizum and A. siphonanthum should be reconsidered.
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Affiliation(s)
- Xiao Fu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Yu-Yang Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xiang-Yi Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, The People's Republic of China.
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Çavuşoğlu D. Modulation of NaCl-induced osmotic, cytogenetic, oxidative and anatomic damages by coronatine treatment in onion (Allium cepa L.). Sci Rep 2023; 13:1580. [PMID: 36709377 PMCID: PMC9884239 DOI: 10.1038/s41598-023-28849-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Coronatine (COR), a bacterial phytotoxin produced by Pseudomonas syringae, plays important roles in many plant growth processes. Onion bulbs were divided four groups to investigate the effects of COR against sodium chloride (NaCl) stress exposure in Allium cepa L. root tips. While control group bulbs were soaked in tap water medium, treatment group bulbs were grown in 0.15 M NaCl, 0.01 µM COR and 0.01 µM COR + 0.15 M NaCl medium, respectively. NaCl stress seriously inhibited the germination, root lenght, root number and fresh weight of the bulbs. It significantly decreased the mitotic index (MI), whereas dramatically increased the micronucleus (MN) frequency and chromosomal aberrations (CAs). Moreover, in order to determine the level of lipid peroxidation occurring in the cell membrane, malondialdehyde (MDA) content was measured and it was determined that it was at the highest level in the group germinated in NaCl medium alone. Similarly, it was revealed that the superoxide dismutase (SOD), catalase (CAT) and free proline contents in the group germinated in NaCl medium alone were higher than the other groups. On the other hand, NaCl stress caused significant injuries such as epidermis/cortex cell damage, MN formation in epidermis/cortex cells, flattened cells nuclei, unclear vascular tissue, cortex cell wall thickening, accumulation of certain chemical compounds in cortex cells and necrotic areas in the anatomical structure of bulb roots. However, exogenous COR application significantly alleviated the negative effects of NaCl stress on bulb germination and growth, antioxidant defense system, cytogenetic and anatomical structure. Thus, it has been proven that COR can be used as a protective agent against the harmful effects of NaCl on onion.
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Affiliation(s)
- Dilek Çavuşoğlu
- Department of Plant and Animal Production, Plant Protection Program, Atabey Vocational High School, Isparta University of Applied Sciences, Isparta, Turkey.
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Khassanov FO, Pulatov S, Asatulloev T, Ergashov I, Tojibaev KS, Yusupov Z. Alliumsunhangii - a new species from section Brevidentia F.O.Khass. & Iengal. (Amaryllidaceae) from Southern Pamir-Alay, Uzbekistan. PHYTOKEYS 2023; 219:35-48. [PMID: 37252455 PMCID: PMC10209640 DOI: 10.3897/phytokeys.219.96464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/03/2023] [Indexed: 05/31/2023]
Abstract
A new species, Alliumsunhangiisp. nov., of the Middle Asiatic section Brevidentia F.O.Khass. & Iengal., (subgenusAllium, tribe Allioideae, Amaryllidaceae) is described. The species is a small plant from the Babatag Ridge in the Surkhandarya province of Uzbekistan. It is morphologically close to Alliumbrevidens Vved. in having initially dark violet filaments and three-cuspidate inner filaments, but differs by its small size and visibly unequal tepals as well as in the phylogenetic analysis based on ITS data.
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Affiliation(s)
- Furkat O. Khassanov
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
| | - Sardorjon Pulatov
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
| | - Temur Asatulloev
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of Sciences, Beijing, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Ibrokhimjon Ergashov
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of Sciences, Beijing, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Komiljon Sh. Tojibaev
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
| | - Ziyoviddin Yusupov
- Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent 100125, UzbekistanInstitute of Botany, Academy of Sciences of UzbekistanTashkentUzbekistan
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum. Sci Rep 2022; 12:21676. [PMID: 36522492 PMCID: PMC9755143 DOI: 10.1038/s41598-022-26354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.
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Wang L, Zhang C, Yin W, Wei W, Wang Y, Sa W, Liang J. Single-molecule real-time sequencing of the full-length transcriptome of purple garlic (Allium sativum L. cv. Leduzipi) and identification of serine O-acetyltransferase family proteins involved in cysteine biosynthesis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:2864-2873. [PMID: 34741310 DOI: 10.1002/jsfa.11627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Garlic (Allium sativum L.), whose bioactive components are mainly organosulfur compounds (OSCs), is a herbaceous perennial widely consumed as a green vegetable and a condiment. Yet, the metabolic enzymes involved in the biosynthesis of OSCs are not identified in garlic. RESULTS Here, a full-length transcriptome of purple garlic was generated via PacBio and Illumina sequencing, to characterize the garlic transcriptome and identify key proteins mediating the biosynthesis of OSCs. Overall, 22.56 Gb of clean data were generated, resulting in 454 698 circular consensus sequence (CCS) reads, of which 83.4% (379 206) were identified as being full-length non-chimeric reads - their further transcript clustering facilitated identification of 36 571 high-quality consensus reads. Once corrected, their genome-wide mapping revealed that 6140 reads were novel isoforms of known genes, and 2186 reads were novel isoforms from novel genes. We detected 1677 alternative splicing events, finding 2902 genes possessing either two or more poly(A) sites. Given the importance of serine O-acetyltransferase (SERAT) in cysteine biosynthesis, we investigated the five SERAT homologs in garlic. Phylogenetic analysis revealed a three-tier classification of SERAT proteins, each featuring a serine acetyltransferase domain (N-terminal) and one or two hexapeptide transferase motifs. Template-based modeling showed that garlic SERATs shared a common homo-trimeric structure with homologs from bacteria and other plants. The residues responsible for substrate recognition and catalysis were highly conserved, implying a similar reaction mechanism. In profiling the five SERAT genes' transcript levels, their expression pattern varied significantly among different tissues. CONCLUSION This study's findings deepen our knowledge of SERAT proteins, and provide timely genetic resources that could advance future exploration into garlic's genetic improvement and breeding. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, College of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Chao Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, College of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Wei Yin
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
| | - Wei Wei
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
| | - Yonghong Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Wei Sa
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, College of Agriculture and Forestry Sciences, Qinghai University, Xining, China
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11
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Comparative Plastome Analysis of Three Amaryllidaceae Subfamilies: Insights into Variation of Genome Characteristics, Phylogeny, and Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3909596. [PMID: 35372568 PMCID: PMC8970886 DOI: 10.1155/2022/3909596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/19/2022] [Accepted: 02/05/2022] [Indexed: 11/17/2022]
Abstract
In the latest APG IV classification system, Amaryllidaceae is placed under the order of Asparagus and includes three subfamilies: Agapanthoideae, Allioideae, and Amaryllidoideae, which include many economically important crops. With the development of molecular phylogeny, research on the phylogenetic relationship of Amaryllidaceae has become more convenient. However, the current comparative analysis of Amaryllidaceae at the whole chloroplast genome level is still lacking. In this study, we sequenced 18 Allioideae plastomes and combined them with publicly available data (a total of 41 plastomes), including 21 Allioideae species, 1 Agapanthoideae species, 14 Amaryllidoideae species, and 5 Asparagaceae species. Comparative analyses were performed including basic characteristics of genome structure, codon usage, repeat elements, IR boundary, and genome divergence. Phylogenetic relationships were detected using single-copy genes (SCGs) and ribosomal internal transcribed spacer sequences (ITS), and the branch-site model was also employed to conduct the positive selection analysis. The results indicated that all Amaryllidaceae species showed a highly conserved typical tetrad structure. The GC content and five codon usage indexes in Allioideae species were lower than those in the other two subfamilies. Comparison analysis of Bayesian and ML phylogeny based on SCGs strongly supports the monophyly of three subfamilies and the sisterhood among them. Besides, positively selected genes (PSGs) were detected in each of the three subfamilies. Almost all genes with significant posterior probabilities for codon sites were associated with self-replication and photosynthesis. Our study investigated the three subfamilies of Amaryllidaceae at the whole chloroplast genome level and suggested the key role of selective pressure in the adaptation and evolution of Amaryllidaceae.
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Xie DF, Cheng RY, Price M, Chen JP, Lei JQ, Zhang YY, He XJ. Alliumheterophyllum (Amaryllidaceae), a new species from Henan, China. PHYTOKEYS 2022; 190:53-67. [PMID: 35437376 PMCID: PMC8881438 DOI: 10.3897/phytokeys.190.77449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Alliumheterophyllum D.F.Xie & X.J.He, sp. nov. (Amaryllidaceae), is a new species from Henan, China and is described based on morphological and molecular evidence. It is morphologically most similar to A.dumebuchum in the rhomboid scape in cross-section. However, distinctive differences were detected in perianth color, leaf shape and cross-section, flowers' density as well as flowering season. Similarly, the karyotype of A.heterophyllum is 2n = 2x = 16 and in A.dumebuchum is 2n = 4x = 32. Phylogenetic analysis based on nuclear ribosomal Internal Transcribed Spacers (ITS) and three cpDNA regions strongly supports that A.heterophyllum is a member of Allium section Rhizirideum and sister to the other species of this section (e.g. A.senescens, A.spirale, and A.prostratum). Currently, only one population and approximately 120 individuals were discovered; the development of scenic spots in this region may affect its growth and threaten this population. Therefore, this new species is preliminarily considered as Near Threatened (NT) according to criteria of the IUCN Red List.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
| | - Rui-Yu Cheng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, ChinaSichuan UniversityChengduChina
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
| | - Jia-Qing Lei
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
| | - Yi-Yang Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, ChinaSichuan UniversityChengduChina
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13
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Feng B, Wang X, Chen S, Zhang Y, Su X, Song S. Transcriptome analysis and genetic diversity of Allium victorialis germplasms from the Changbai Mountains. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2915-2923. [PMID: 34553046 PMCID: PMC8451692 DOI: 10.1080/23802359.2021.1972857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Changbai Mountains comprise one of the main distribution areas of A. victorialis in China, and this species is endangered owing to habitat changes and overexploitation. However, A. victorialis germplasms have not been systematically collected and studied. The aims of this study were to obtain some detailed genetic information, analyze the genetic diversity, and further promote the protection of A. victorialis germplasms from the Changbai Mountains. Transcriptomic analysis was performed with six A. victorialis samples collected from the Changbai Mountains. At least 146,759 genes for each sample were obtained after performing de novo assembly of the RNA-seq data, and at least 92% of these genes were found to have only one mRNA isoform. These sequences and their functional annotations provided a large-scale genetic resource of this species. Phylogenetic analysis showed that A. victorialis was genetically distant from some related species, e.g. Allium sativum, Allium fistulosum, and Allium cepa, but genetically close to Allium tuberosum. The two A. victorialis var. listera samples were phylogenetically separated from the other four samples, and these two samples should be regarded as Allium listera. In addition, two KASP markers for discriminating the Dongfeng samples from the other four A. victorialis samples were successfully developed. This study lays the foundation for future studies on the genetic diversity and evolution of Allium species, as well as for the conservation of A. victorialis germplasms from the Changbai Mountains and other populations of this species.
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Affiliation(s)
- Bo Feng
- Jilin Agricultural University, Changchun, Jilin, China.,Jilin Provincial Academy of Forestry Sciences, Changchun, Jilin, China
| | - Xiufeng Wang
- Jilin Academy of Vegetable and Flower Sciences, Changchun, Jilin, China
| | - Shanshan Chen
- Jilin Agricultural University, Changchun, Jilin, China
| | - Yue Zhang
- Jilin Academy of Vegetable and Flower Sciences, Changchun, Jilin, China
| | - Xuejiao Su
- Jilin Agricultural University, Changchun, Jilin, China
| | - Shuyao Song
- Jilin Agricultural University, Changchun, Jilin, China
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14
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Li MJ, Yu HX, Guo XL, He XJ. Out of the Qinghai-Tibetan Plateau and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae). AOB PLANTS 2021; 13:plab017. [PMID: 34055281 PMCID: PMC8152445 DOI: 10.1093/aobpla/plab017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidated the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the Qinghai-Tibetan Plateau (QTP) and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4-3 million years ago (Mya). Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.
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Affiliation(s)
- Min-Jie Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, P.R. China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
- Nanjing Institute of Environmental Science, MEE, Nanjing, Jiangsu 210042, P.R. China
| | - Xian-Lin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, P.R. China
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15
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Seed Morphology of Allium L. (Amaryllidaceae) from Central Asian Countries and Its Taxonomic Implications. PLANTS 2020; 9:plants9091239. [PMID: 32962259 PMCID: PMC7570352 DOI: 10.3390/plants9091239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 11/18/2022]
Abstract
We studied seed macro- and micro-morphological characteristics of 48 Allium species (51 accessions) belonging to 24 sections and 7 subgenera. Our taxonomic sampling focused on the central Asian regions of Uzbekistan, Kyrgyzstan, and Mongolia. The seed length ranged between 1.74 ± 0.16–4.47 ± 0.43 mm and width ranged between 1.06 ± 0.08–3.44 ± 0.23 mm, showing various shapes. The irregular and elongated polygonal testa cells occurred in all investigated species. Seed testa sculptures showed high variation in their anticlinal walls associated with different shapes: straight to with U-, S- or Omega-type undulations among the species. The moderately flat to convex periclinal walls with various sized verrucae or granules were found in all investigated taxa. Based on our research, we conclude that seed characteristics such as size, shape, and the seed testa features show their significant variability, revealing key characteristics to support taxonomic relationships and major clades recovered in the molecular phylogeny of the genus Allium. Especially, the anticlinal wall characteristics were highly variable and decisive at the both section and species levels. In addition, widely varied shapes and sizes of the seeds were remarkably effective to distinguish Allium species.
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16
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Sun X, Zhu S, Li N, Cheng Y, Zhao J, Qiao X, Lu L, Liu S, Wang Y, Liu C, Li B, Guo W, Gao S, Yang Z, Li F, Zeng Z, Tang Q, Pan Y, Guan M, Zhao J, Lu X, Meng H, Han Z, Gao C, Jiang W, Zhao X, Tian S, Su J, Cheng Z, Liu T. A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis. MOLECULAR PLANT 2020; 13:1328-1339. [PMID: 32730994 DOI: 10.1016/j.molp.2020.07.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/26/2020] [Accepted: 07/27/2020] [Indexed: 05/21/2023]
Abstract
Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds. Here, we report a chromosome-level genome assembly for garlic, with a total size of approximately 16.24 Gb, as well as the annotation of 57 561 predicted protein-coding genes, making garlic the first Allium species with a sequenced genome. Analysis of this garlic genome assembly reveals a recent burst of transposable elements, explaining the substantial expansion of the garlic genome. We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans, and provided new insights into the biosynthesis of these two compounds. Furthermore, a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs. The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.
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Affiliation(s)
- Xiudong Sun
- Shandong Agricultural University, Tai'an 271018, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Ningyang Li
- Shandong Agricultural University, Tai'an 271018, China
| | - Yi Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Jing Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xuguang Qiao
- Shandong Agricultural University, Tai'an 271018, China
| | - Li Lu
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Shiqi Liu
- Shandong Agricultural University, Tai'an 271018, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Chan Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Benping Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wu Guo
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Shuang Gao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Yupeng Pan
- Northwest A&F University, Yangling 712100, China
| | - Mengjiao Guan
- Shandong Agricultural University, Tai'an 271018, China
| | - Jian Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xiaoming Lu
- Shandong Agricultural University, Tai'an 271018, China
| | - Huanwen Meng
- Northwest A&F University, Yangling 712100, China
| | - Zhenlin Han
- Shandong Agricultural University, Tai'an 271018, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
| | - Zhihui Cheng
- Northwest A&F University, Yangling 712100, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China.
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17
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Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8542797. [PMID: 32626767 PMCID: PMC7306069 DOI: 10.1155/2020/8542797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/22/2020] [Indexed: 11/20/2022]
Abstract
The section Pallasia is one of the components of the genus Allium subgenus Allium (Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect. Pallasia species were reported, and a comparative analysis was performed with other three related Allium species. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (except Allium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary, A. pallasii exhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eight Allium species cluster into a group, and A. pallasii exhibit a close relationship with A. obliquum. Higher pairwise Ka/Ks ratios were found in A. schoenoprasoides compared to A. caeruleum and A. macrostemon while a lower value of Ka/Ks ratios was detected between A. caeruleum and A. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research in Allium.
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18
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Xie DF, Tan JB, Yu Y, Gui LJ, Su DM, Zhou SD, He XJ. Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences. ANNALS OF BOTANY 2020; 125:1039-1055. [PMID: 32239179 PMCID: PMC7262478 DOI: 10.1093/aob/mcaa024] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. METHODS In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. RESULTS Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. CONCLUSIONS Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Jin-Bo Tan
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Lin-Jian Gui
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, People’s Republic of China
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19
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Sayadi V, Karimzadeh G, Rashidi Monfared S, Naghavi MR. Identification and expression analysis of S-alk(en)yl-L-cysteine sulfoxide lyase isoform genes and determination of allicin contents in Allium species. PLoS One 2020; 15:e0228747. [PMID: 32092058 PMCID: PMC7039512 DOI: 10.1371/journal.pone.0228747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/21/2020] [Indexed: 11/19/2022] Open
Abstract
Alliinase is the key enzyme in allicin biosynthesis pathway. In the current study, the identification and sequencing of alliinase genes along with determination of allicin contents were reported for Allium species with a novel report for Iranian endemic species. The presence of different isoforms in the Allium being discovered for the first time. In bulbs tissue, the highest allicin concentration was in Allium sativum, A. umbilicatum, and A. fistolosum (1.185%, 0.367%, and 0.34%, respectively), followed by A. spititatum (0.072%), A. lenkoranicum (0.055%), A. atroviolaseum (0.36%), A. rubellum (0.041%), and A. stamineum (0.007%). The highest allicin content in the leaves and roots were in A. sativum (0.13%), and A. stamineum (0.195%), respectively. The ORFs length ranged from 1416 in A. sativum (iso-alliinase2; ISA2) to 1523 bp in A. sativum (alliinase); the identity with A. sativum (alliinase) varies from 95% to 68% for A. ampeloprasum, and A. sativum (iso-alliinase1, ISA1) respectively. These data suggested that both ISA1 and ISA2 had a high expression in the roots and bulbs compared to A. sativum as the control in all species. Note that ISA1 and ISA2 were not expressed in the leaves. The results showed that isoforms expression patterns among different tissues in Allium species were variable. The presence of various isoforms is a possible explanation for the difference between the species in terms of obtained results, especially the amount of allicin.
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Affiliation(s)
- Vahid Sayadi
- Faculty of Agriculture, Department of Plant Genetics and Breeding, Tarbiat Modares University, Tehran, Iran
| | - Ghasem Karimzadeh
- Faculty of Agriculture, Department of Plant Genetics and Breeding, Tarbiat Modares University, Tehran, Iran
- * E-mail:
| | - Sajad Rashidi Monfared
- Faculty of Agriculture, Department of Agricultural Biotechnology, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Reza Naghavi
- Agronomy and Plant Breeding Department, Agricultural College, University of Tehran, Karaj, Iran
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20
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Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing. Mol Phylogenet Evol 2020; 146:106737. [PMID: 31982455 DOI: 10.1016/j.ympev.2020.106737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 01/27/2023]
Abstract
Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.
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21
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Han TS, Zheng QJ, Onstein RE, Rojas-Andrés BM, Hauenschild F, Muellner-Riehl AN, Xing YW. Polyploidy promotes species diversification of Allium through ecological shifts. THE NEW PHYTOLOGIST 2020; 225:571-583. [PMID: 31394010 DOI: 10.1111/nph.16098] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/01/2019] [Indexed: 05/14/2023]
Abstract
Despite the role of polyploidy in multiple evolutionary processes, its impact on plant diversification remains controversial. An increased polyploid frequency may facilitate speciation through shifts in ecology, morphology or both. Here we used Allium to evaluate: (1) the relationship between intraspecific polyploid frequency and species diversification rate; and (2) whether this process is associated with habitat and/or trait shifts. Using eight plastid and nuclear ribosomal markers, we built a phylogeny of 448 Allium species, representing 46% of the total. We quantified intraspecific ploidy diversity, heterogeneity in diversification rates and their relationship along the phylogeny using trait-dependent diversification models. Finally, we evaluated the association between polyploidisation and habitat or trait shifts. We detected high ploidy diversity in Allium and a polyploidy-related diversification rate shift with a probability of 95% in East Asia. Allium lineages with high polyploid frequencies had higher species diversification rates than those of diploids or lineages with lower polyploid frequencies. Shifts in speciation rates were strongly correlated with habitat shifts linked to particular soil conditions; 81.7% of edaphic variation could be explained by polyploidisation. Our study emphasises the role of intraspecific polyploid frequency combined with ecological drivers on Allium diversification, which may explain plant radiations more generally.
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Affiliation(s)
- Ting-Shen Han
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Quan-Jing Zheng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Blanca M Rojas-Andrés
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Alexandra N Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Leipzig University, Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Yao-Wu Xing
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses. Sci Rep 2019; 9:12250. [PMID: 31439882 PMCID: PMC6706373 DOI: 10.1038/s41598-019-48708-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022] Open
Abstract
The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium. We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium.
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Jin FY, Y X, Xie DF, Li H, Yu Y, Zhou SD, He XJ. Comparative Complete Chloroplast Genome Analyses and Contribution to the Understanding of Chloroplast Phylogeny and Adaptive Evolution in Subgenus Anguinum. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome. FRONTIERS IN PLANT SCIENCE 2019; 10:460. [PMID: 31114591 PMCID: PMC6503222 DOI: 10.3389/fpls.2019.00460] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuan Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Filyushin MA, Mazur AM, Shchennikova AV, Kochieva ЕZ. Comparative analysis of the complete plastomes of garlic Allium sativum and bulb onion Allium cepa. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sequencing and comparative characterization of plant plastid genomes, or plastomes, is an important tool for modern phylogenetic and taxonomic studies, as well as for understanding the plastome evolution. The genusAlliumL. (family Amaryllidaceae) incorporates more than 900 species, includes economically significant vegetable crops such as garlicA. sativum, onionA. cepa, leekA. porrum, etc. In this work, the plastome of garlicA. sativumhas been completely sequenced. TheA. sativumplastome is 153172 bp in size. It consists of a large unique (LSC, 82035 bp) and small unique (SSC, 18015 bp) copies, separated by inverted repeats (IRa and IRb) of 26561 bp each. In the garlic plastome, 134 genes have been annotated: 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 6 pseudogenes. Comparative analysis ofA. sativumandA. cepaplastomes reveals differences in the sizes of structural elements and spacers at the inverted repeat boundaries. The total numbers of genes inA. sativumandA. cepaare the same, but the gene composition is different: therpl22gene is functional inA. sativum, being a pseudogene inA. cepa; conversely, therps16gene is a pseudogene inA. sativumand a protein-coding gene inA. cepa. In theA. sativumandA. cepaplastomes, 32 SSR sequences have been identified. More than half of them are dinucleotides, and the remaining are tetra-, penta-, and hexanucleotides at the same time, trinucleotides were absent. The compared plastomes differ in the numbers of certain SSRs, and some are present in only one of the species.
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26
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Tanaka E, Ono Y. Whole-leaf fluorescence imaging to visualize in planta fungal structures of Victory onion leaf rust fungus, Uromyces japonicus, and its taxonomic evaluation. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jin FY, Xie DF, Zhou SD, He XJ. Characterization of the complete chloroplast genome of Allium prattii. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:153-154. [PMID: 33490492 PMCID: PMC7800986 DOI: 10.1080/23802359.2018.1436994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The genus Allium is one of the world's largest monocot genera. However, few reports on the complete chloroplast genome of Allium plants are reported. In this study, we reported the complete chloroplast genome of Allium prattii. The genome sequence was 154,482 bp in length, including a large single copy region (LSC) of 83,392 bp and a small single copy region (SSC) of 18,064 bp, which were separated by two inverted repeat (IR) regions of 26,513 bp. The complete chloroplast genome contains 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with several reported chloroplast genomes showed that A. prattii has a close genetic relationship with A. cepa and A. sativum.
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Affiliation(s)
- Fang-Yu Jin
- Country Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Deng-Feng Xie
- Country Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Song-Dong Zhou
- Country Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Xing-Jin He
- Country Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
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Danderson CA, Downie SR, Hermann M. Rampant polyphyly in the Arracacia clade (Apiaceae) and an assessment of the phylogenetic utility of 20 noncoding plastid loci. Mol Phylogenet Evol 2017; 118:286-305. [PMID: 29017853 DOI: 10.1016/j.ympev.2017.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
Abstract
The Arracacia clade (Apiaceae, Apioideae) is a heterogeneous assemblage of 12 genera, comprising 111 known species distributed in high montane temperate and sub-alpine habitats of meso- and South America. Previous studies have indicated that the genera Arracacia, Coulterophytum, and Prionosciadium are polyphyletic, but for the most part relationships among the members of the clade are largely unknown. Initially, cladistic analyses of nrDNA ITS sequences were carried out on 212 accessions (122 taxa), representing 92 species of the Arracacia clade and outgroups from the closely-related páramo genera Cotopaxia, Niphogeton, and Perissocoeleum and members of the Perennial Endemic North American clade and its allies. Using the ITS results to inform sampling of a small subset of taxa, a pilot study examining the phylogenetic utility of 20 noncoding chloroplast loci was subsequently performed to identify those regions most useful at resolving relationships. A cost-benefit analysis determined that five loci (trnQ-5'rps16, trnD-trnT, rpl32-trnL, psbD-trnT, ndhA intron) would maximize resolution and branch support in the clade. Cladistic analyses of four of these loci (trnQ-5'rps16, trnD-trnT, rpl32-trnL, ndhA intron) and the ITS region, separately and combined, revealed that Arracacia, Coaxana, Coulterophytum, Prionosciadium, and Rhodosciadium are each polyphyletic and that Donnellsmithia and Myrrhidendron are each monophyletic. Although most relationships in the Arracacia clade and among the closely-related genera Cotopaxia, Niphogeton, and Perissocoeleum are poorly resolved and supported, ten groups are recognized for future revisionary studies. Polyploidy and rapid species radiation have likely confounded generic circumscriptions and interpretation of relationships.
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Affiliation(s)
- Clark A Danderson
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Hauenschild F, Favre A, Schnitzler J, Michalak I, Freiberg M, Muellner-Riehl AN. Spatio-temporal evolution of Allium L. in the Qinghai-Tibet-Plateau region: Immigration and in situ radiation. PLANT DIVERSITY 2017; 39:167-179. [PMID: 30159508 PMCID: PMC6112296 DOI: 10.1016/j.pld.2017.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/11/2017] [Accepted: 05/31/2017] [Indexed: 05/23/2023]
Abstract
A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes (orogenesis) and a biological response (diversification). Yet, a substantial delay (up to 30 Myr) between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau (QTP) region: (1) While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, (2) QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of Allium. Our study therefore adds to the growing evidence supporting the "mountain-geo-biodiversity hypothesis", which highlights the role of climate oscillations for the diversification of mountain organisms.
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Affiliation(s)
- Frank Hauenschild
- Leipzig University, Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Johannisallee 21–23, 04103 Leipzig, Germany
| | - Adrien Favre
- Leipzig University, Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Johannisallee 21–23, 04103 Leipzig, Germany
| | - Jan Schnitzler
- Leipzig University, Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Johannisallee 21–23, 04103 Leipzig, Germany
| | - Ingo Michalak
- Leipzig University, Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Johannisallee 21–23, 04103 Leipzig, Germany
| | - Martin Freiberg
- Leipzig University, Department of Systematic Botany and Functional Biodiversity Research, Johannisallee 21–23, 04103 Leipzig, Germany
| | - Alexandra N. Muellner-Riehl
- Leipzig University, Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Johannisallee 21–23, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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30
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Zhu S, Tang S, Tan Z, Yu Y, Dai Q, Liu T. Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium. BMC Genomics 2017; 18:60. [PMID: 28068920 PMCID: PMC5223570 DOI: 10.1186/s12864-016-3474-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 12/26/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fistular leaves frequently appear in Allium species, and previous developmental studies have proposed that the process of fistular leaf formation involves programmed cell death. However, molecular evidence for the role of programmed cell death in the formation of fistular leaf cavities has yet to be reported. RESULTS In this study, we characterized the leaf transcriptomes of nine Allium species, including six fistular- and three solid-leaved species. In addition, we identified orthologous genes and estimated their Ka and Ks values, in order to ascertain their selective pattern. Phylogenetic analysis based on the transcriptomes revealed that A. tuberosum was the most ancestral among the nine species, and analysis of orthologous genes between A. tuberosum and the other eight species indicated that 149 genes were subject to positive selection; whereas >3000 had undergone purifying selection in each species. CONCLUSIONS We found that many genes that are potentially related to programmed cell death either exhibited rapid diversification in fistular-leaved species, or were conserved in solid-leaved species in evolutionary history. These genes potentially involved in programmed cell death might play important roles in the formation of fistular leaf cavities in Allium, and the differing selection patterns in fistular- and solid-leaved species may be responsible for the evolution of fistular leaves.
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Affiliation(s)
- Siyuan Zhu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Shouwei Tang
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zhijian Tan
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yongting Yu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Touming Liu
- Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
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