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Zhang T, Huang S, Song S, Zou M, Yang T, Wang W, Zhou J, Liao H. Identification of evolutionary relationships and DNA markers in the medicinally important genus Fritillaria based on chloroplast genomics. PeerJ 2022; 9:e12612. [PMID: 35003925 PMCID: PMC8684722 DOI: 10.7717/peerj.12612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/18/2021] [Indexed: 02/04/2023] Open
Abstract
The genus Fritillaria has attracted great attention because of its medicinal and ornamental values. At least three reasons, including the accurate discrimination between various Fritillaria species, protection and sustainable development of rare Fritillaria resources as well as understanding of relationship of some perplexing species, have prompted phylogenetic analyses and development of molecular markers for Fritillaria species. Here we determined the complete chloroplast (CP) genomes for F. unibracteata, F. przewalskii, F. delavayi, and F. sinica through Illumina sequencing, followed by de novo assembly. The lengths of the genomes ranged from 151,076 in F. unibracteata to 152,043 in F. przewalskii. Those CP genomes displayed a typical quadripartite structure, all including a pair of inverted repeats (26,078 to 26,355 bp) separated by the large single-copy (81,383 to 81,804 bp) and small single-copy (17,537 to 17,569 bp) regions. Fritillaria przewalskii, F. delavayi, and F. sinica equivalently encoded 133 unique genes consisting of 38 transfer RNA genes, eight ribosomal RNA genes, and 87 protein coding genes, whereas F. unibracteata contained 132 unique genes due to absence of the rps16 gene. Subsequently, comparative analysis of the complete CP genomes revealed that ycf1, trnL, trnF, ndhD, trnN-trnR, trnE-trnT, trnN, psbM-trnD, atpI, and rps19 to be useful molecular markers in taxonomic studies owning to their interspecies variations. Based on the comprehensive CP genome data collected from 53 species in Fritillaria and Lilium genera, a phylogenomic study was carried out with three Cardiocrinum species and five Amana species as outgroups. The results of the phylogenetic analysis showed that Fritillaria was a sister to Lilium, and the interspecies relationships within subgenus Fritillaria were well resolved. Furthermore, phylogenetic analysis based on the CP genome was proved to be a promising method in selecting potential novel medicinal resources to substitute current medicinal species that are on the verge of extinction.
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Affiliation(s)
- Tian Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Sipei Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Simin Song
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Meng Zou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Tiechui Yang
- Qinghai lvkang Biological Development Co., Ltd, Xining, Qinghai, China
| | - Weiwei Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Jiayu Zhou
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Hai Liao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
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Roguz K, Hill L, Roguz A, Zych M. Evolution of Bird and Insect Flower Traits in Fritillaria L. (Liliaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:656783. [PMID: 33868353 PMCID: PMC8044542 DOI: 10.3389/fpls.2021.656783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/03/2021] [Indexed: 05/27/2023]
Abstract
Pollinators are often perceived as a primary selective agent influencing flower traits such as colour, size, and nectar properties. The genus Fritillaria L. (Liliaceae), comprising approximately 150 species, is described as generally insect pollinated. However, there are at least three exceptions: two hummingbird-pollinated North American species and one passerine-pollinated Asian species. Despite this variation in pollination, little is known about flower traits that may accompany this shift in fritillaries. In this study, we aimed to assess the attractiveness of the floral traits for (new) pollinators and track the evolution of flowers traits in the context of a shift in the principal pollinator. Therefore, we studied 14 flower traits related to the pollination in 60 Fritillaria species and traced the evolutionary trajectory of these traits. We used a phylogenetic tree of the genus, based on five DNA markers (matK, rpl16, and rbcL, 18S, and ITS) to reconstruct the ancestral state of studied flower traits. The results show that in bird-pollinated species several new traits evolved. For example, flower colouration, nectar sugar, and amino acid concentration and composition fulfil the criteria of ornithophilous flowers, although flower traits do not exclude insect pollinators in bird-pollinated fritillaries. Interestingly, we recorded potential reversals from bird to insect pollination. Our analysis, showing a broad study of flower traits among closely related species in the context of pollinator shift, serves as a starting point for future work exploring the genetic and physiological mechanisms controlling flower traits in the genus Fritillaria.
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Affiliation(s)
- Katarzyna Roguz
- Botanic Garden, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | | | - Marcin Zych
- Botanic Garden, Faculty of Biology, University of Warsaw, Warsaw, Poland
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Chen Q, Wu X, Zhang D. Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PeerJ 2019; 7:e7480. [PMID: 31497389 PMCID: PMC6708372 DOI: 10.7717/peerj.7480] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/15/2019] [Indexed: 01/23/2023] Open
Abstract
Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
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Affiliation(s)
- Qi Chen
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Xiaobo Wu
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy and Chemistry, Dali University, Dali, Yunnan, China.,Institute of Materia Medica, Dali University, Dali, Yunnan, China
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Complete chloroplast genome of seven Fritillaria species, variable DNA markers identification and phylogenetic relationships within the genus. PLoS One 2018; 13:e0194613. [PMID: 29543905 PMCID: PMC5854438 DOI: 10.1371/journal.pone.0194613] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023] Open
Abstract
Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences. These were compared to previously sequenced Fritillaria cp genomes. Phylogenetic analysis was then used to evaluate the relationships of the Xinjiang species and assess the evolution of an undivided stigma. The seven cp genomes ranged from 151,764 to 152,112 bp, presenting a traditional quadripartite structure. The gene order and gene content of the seven cp genomes were identical. A comparison of the 13 cp genomes indicated that the structure is highly conserved. Ten highly divergent regions were identified that could be valuable in phylogenetic and population genetic studies. The phylogenetic relationships of the 13 Fritillaria species inferred from the protein-coding genes, large single-copy, small single-copy, and inverted repeat regions were identical and highly resolved. The phylogenetic relationships of the species corresponded with their geographic distribution patterns, in that the north group (consisting of eight species from Xinjiang and Heilongjiang in North China) and the south group (including six species from South China) were basically divided at 40°N. Species with an undivided stigma were not monophyletic, suggesting that this trait might have evolved several times in the genus.
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Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria. Sci Rep 2018; 8:1184. [PMID: 29352182 PMCID: PMC5775360 DOI: 10.1038/s41598-018-19591-9] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People’s Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.
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Yang Y, Fan X, Wang L, Zhang HQ, Sha LN, Wang Y, Kang HY, Zeng J, Yu XF, Zhou YH. Phylogeny and maternal donors of Elytrigia Desv. sensu lato (Triticeae; Poaceae) inferred from nuclear internal-transcribed spacer and trnL-F sequences. BMC PLANT BIOLOGY 2017; 17:207. [PMID: 29157213 PMCID: PMC5697114 DOI: 10.1186/s12870-017-1163-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial. We used nuclear internal-transcribed spacer (nrITS) sequences and chloroplast trnL-F region to study the relationships of phylogenetic and maternal genome donor of Elytrigia Desv. sensu lato. RESULTS (1) E, F, P, St, and W genomes bear close relationship with one another and are distant from H and Ns genomes. Ee and Eb are homoeologous. (2) In ESt genome species, E genome is the origin of diploid Elytrigia species with E genome, St genome is the origin of Pseudoroegneria. (3) Diploid species Et. elongata were differentiated. (4) Et. stipifolia and Et. varnensis sequences are diverse based on nrITS data. (5) Et. lolioides contains St and H genomes and belongs to Elymus s. l. (6) E genome diploid species in Elytrigia serve as maternal donors of E genome for Et. nodosa (PI547344), Et. farcta, Et. pontica, Et. pycnantha, Et. scirpea, and Et. scythica. At least two species act as maternal donor of allopolyploids (ESt and EStP genomes). CONCLUSIONS Our results suggested that Elytrigia s. l. species contain different genomes, which should be divided into different genera. However, the genomes of Elytrigia species had close relationships with one another. Diploid species were differentiated, because of introgression and different geographical sources. The results also suggested that the same species and the same genomes of different species have different maternal donor. Further study of molecular biology and cytology could facilitate the evaluation of our results of phylogenetic in a more specific and accurate way.
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Affiliation(s)
- Yan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009 Sichuan People’s Republic of China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Long Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Xiao-Fang Yu
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
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Kiani M, Mohammadi S, Babaei A, Sefidkon F, Naghavi MR, Ranjbar M, Razavi SA, Saeidi K, Jafari H, Asgari D, Potter D. Iran supports a great share of biodiversity and floristic endemism for Fritillaria spp. (Liliaceae): A review. PLANT DIVERSITY 2017; 39:245-262. [PMID: 30159518 PMCID: PMC6112302 DOI: 10.1016/j.pld.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 05/28/2023]
Abstract
Iran supports a great share of exotic and/or endemic plant genera and species. The genus Fritillaria (Liliaceae) is a precious part of this botanical richness with 19 species, of which 10 are endemic to the country. However, signs are mounting that the country is truly at a crossroads when it comes to preservation of this national wealth. In this regard, an effective conservation strategy should thoroughly consider the classification of Fritillaria, as conservation practices are compromised by knowledge gaps in systematics and taxonomy. As published studies on Fritillaria in Iran have been sporadic and limited in scope, the aim of this review is to provide information necessary to help bridge these information gaps. Our objective is to facilitate increased understanding of the geographic, taxonomic, cytogenetic and phylogenetic status of Iranian Fritillaria, which is vital to meeting the goal of sustainable conservation of the genus in Iran and neighboring areas.
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Affiliation(s)
- Mahmoud Kiani
- Department of Biotechnology & Medicinal Plants, Amol University of Special Modern Technologies, Amol, Iran
| | - Shirin Mohammadi
- Department of Horticultural Science, Shiraz University, Shiraz, Iran
| | - Alireza Babaei
- Department of Horticultural Science, Tarbiat Modares University, Tehran, Iran
| | | | - Mohamad Reza Naghavi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Tehran, Karaj, Iran
| | - Mojtaba Ranjbar
- Department of Biotechnology & Medicinal Plants, Amol University of Special Modern Technologies, Amol, Iran
| | - Seyed Ali Razavi
- Department of Biotechnology & Medicinal Plants, Amol University of Special Modern Technologies, Amol, Iran
| | - Keramatollah Saeidi
- Department of Horticulture, Faculty of Agriculture, Shahre Kord University, Shahre Kord, Iran
| | - Hadi Jafari
- Department of Horticultural Science, Tarbiat Modares University, Tehran, Iran
| | - Davoud Asgari
- Department of Physiology & Breeding of Ornamental Plants, Engineering Faculty of Horticulture Sciences, University of Tehran, Karaj, Iran
| | - Daniel Potter
- Department of Plant Sciences, University of California-Davis, Davis, USA
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Cytoplasmic diversity, phylogenetic relationships and molecular evolution of Tunisian Citrus species as inferred from mutational events and pseudogene of chloroplast trnL-trnF spacer. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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