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Nikolaeva OV, Rusin LY, Mikhailov KV, Aleoshin VV, De Ley P. Both-strand gene coding in a plastome-like mitogenome of an enoplid nematode. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:419-424. [PMID: 38318934 DOI: 10.1002/jez.b.23241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 12/18/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, Campydora demonstrans, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The C. demonstrans mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of cox1 gene as a phylogenetic marker for establishing nematode relationships within higher taxa.
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Affiliation(s)
- Olga V Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Leonid Yu Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Kirill V Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Vladimir V Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Paul De Ley
- Department of Entomology, Plant Pathology & Weed Science, New Mexico State University, Las Cruces, New Mexico, USA
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Liu X, Luo J, Chen H, Li T, Qu T, Tang M, Fu Z. Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis. BMC Genomics 2024; 25:769. [PMID: 39112930 PMCID: PMC11308156 DOI: 10.1186/s12864-024-10663-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The Synotis (C. B. Clarke) C. Jeffrey & Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey & Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey & Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey & Y.L. Chen and S. erythropappa (Bureau & Franch.) C. Jeffrey & Y. L. Chen had been sequenced using next-generation sequencing technology and reported here. RESULTS These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399 bp), the small single-copy regions (SSC, 18,262 to 18,287 bp), and the inverted repeat regions (IR, 24,837 to 24,842 bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae. CONCLUSIONS This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.
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Affiliation(s)
- Xiaofeng Liu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Junjia Luo
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Hui Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tingyu Li
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Tianmeng Qu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Ming Tang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Zhixi Fu
- Key Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University), Ministry of Education, Chengdu, 610066, China.
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China.
- Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University, Chengdu, 610101, China.
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Lin Y, Xiang Y, Wei S, Zhang Q, Liu Y, Zhang Z, Tang S. Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape. Ecol Evol 2024; 14:e70094. [PMID: 39091326 PMCID: PMC11291554 DOI: 10.1002/ece3.70094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.
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Affiliation(s)
- Yanfang Lin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
- Wuzhou No. 18 Middle SchoolWuzhouChina
| | - Yingying Xiang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Sujian Wei
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Yanhua Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of EducationGuangxi Normal UniversityGuilinChina
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River BasinGuangxi Normal UniversityGuilinChina
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Alawfi MS, Alzahrani DA, Albokhari EJ. Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:654. [PMID: 38987665 PMCID: PMC11234707 DOI: 10.1186/s12870-024-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Heliotropiaceae is a family of the order Boraginales and has over 450 species. The members of the family Heliotropiaceae have been widely reported to be used in traditional medicine Over time, the classification of Heliotropiaceae has remained uncertain and has moved from family to subfamily, or conversely. RESULTS In the present study, we sequenced, analyzed, and compared the complete plastomes of Euploca strigosa, Heliotropium arbainense, and Heliotropium longiflorum with the genomes of related taxa. The lengths of the plastomes of E. strigosa, H. arbainense, and H. longiflorum were 155,174 bp, 154,709 bp, and 154,496 bp, respectively. Each plastome consisted of 114 genes: 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The long repeats analysis indicated that reverse, palindromic, complement and forward repeats were all found in the three plastomes. The simple repeats analysis showed that the plastomes of E. strigosa, H. arbainense, and H. longiflorum contained 158, 165, and 151 microsatellites, respectively. The phylogenetic analysis confirmed two major clades in the Boraginales: clade I comprised Boraginaceae, while clade II included Heliotropiaceae, Ehretiaceae, Lennoaceae, and Cordiaceae. Inside the family Heliotropiaceae, E. strigosa is nested within the Heliotropium genus. CONCLUSIONS This study expands our knowledge of the evolutionary relationships within Heliotropiaceae and offers useful genetic resources.
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Affiliation(s)
- Mohammad S Alawfi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia.
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Enas J Albokhari
- Department of Biological Sciences, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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Coello AJ, Vargas P, Alameda‐Martín A, Cano E, Arjona Y, Fernández‐Mazuecos M. Phylogenetic and phylogeographic evidence for the colonization success of the diplochorous Astydamia latifolia across the Canary Islands. Ecol Evol 2024; 14:e11624. [PMID: 38966248 PMCID: PMC11222747 DOI: 10.1002/ece3.11624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/29/2024] [Accepted: 06/10/2024] [Indexed: 07/06/2024] Open
Abstract
Astydamia latifolia is the only species of the genus Astydamia, which forms an early-diverging lineage of Apiaceae, subfamily Apioideae. This species is subendemic to the Canary Islands and one of the most representative species of the coastal environments of this archipelago. Astydamia displays diplochory, that is, diaspores with two long-distance dispersal (LDD) syndromes. In particular, A. latifolia has both anemochorous and thalassochorous fruit traits (corky and winged mericarps). Although we expect this species to have a high dispersal capacity, there is no genetic study addressing it. The divergence time of this species from its sister taxon is also unknown. In this study, we aimed (i) to unveil the phylogenetic relationships and divergence times of A. latifolia; (ii) to reconstruct its phylogeographic structure across the Canary Islands; and (iii) to estimate the number of inter-island colonization events. To these ends, we first sequenced the internal transcribed spacer (ITS) region for A. latifolia, reconstructed the phylogenetic relationships of Astydamia and Apiaceae relatives and estimated divergence times. Then, two plastid DNA regions (psaI-aacD and psbK-trnS) were sequenced for 158 individuals (from 36 Canarian population and one NW African population) to reconstruct a haplotype network. The recently developed method Phylogeographic Analysis of Island Colonization Events (PAICE) was used to estimate the number of inter-island colonization events. Results show that A. latifolia is a phylogenetically isolated lineage that diverged from the most closely related genus (Molopospermum) in the Eocene-Miocene. It displays a low plastid DNA diversity (only four haplotypes detected), which is accompanied by a high degree of haplotype sharing between islands and highly linear rarefaction curves of colonization obtained in PAICE. These findings suggest a high colonization ability for this species, most likely related to the availability of two LDD syndromes.
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Affiliation(s)
- Alberto J. Coello
- Departamento de Biología (Botánica)Universidad Autónoma de MadridMadridSpain
- Real Jardín Botánico (RJB‐CSIC)MadridSpain
- Department of BotanyNational Museum of Natural History, Smithsonian InstitutionWashingtonDCUSA
| | | | - Aitor Alameda‐Martín
- Real Jardín Botánico (RJB‐CSIC)MadridSpain
- Departamento de AgronomíaUniversidad de AlmeríaAlmeríaSpain
| | | | - Yurena Arjona
- Real Jardín Botánico (RJB‐CSIC)MadridSpain
- Department of Botany, Ecology and Plant PhysiologyUniversity of La LagunaSan Cristóbal de La LagunaSpain
| | - Mario Fernández‐Mazuecos
- Departamento de Biología (Botánica)Universidad Autónoma de MadridMadridSpain
- Real Jardín Botánico (RJB‐CSIC)MadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
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Lubna, Asaf S, Khan I, Jan R, Asif S, Bilal S, Kim KM, Al-Harrasi A. Genetic characterization and phylogenetic analysis of the Nigella sativa (black seed) plastome. Sci Rep 2024; 14:14509. [PMID: 38914674 PMCID: PMC11196742 DOI: 10.1038/s41598-024-65073-6] [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: 01/30/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
In this study, the complete plastome sequence of Nigella sativa (black seed), was analyzed for the first time. The plastome spans approximately 154,120 bp, comprising four sections: the Large Single-Copy (LSC) (85,538 bp), the Small Single-Copy (SSC) (17,984 bp), and two Inverted Repeat (IR) regions (25,299 bp). A comparative study of N. sativa's plastome with ten other species from various genera in the Ranunculaceae family reveals substantial structural variations. The contraction of the inverted repeat region in N. sativa influences the boundaries of single-copy regions, resulting in a shorter plastome size than other species. When comparing the plastome of N. sativa with those of its related species, significant divergence is observed, particularly except for N. damascena. Among these, the plastome of A. glaucifolium displays the highest average pairwise sequence divergence (0.2851) with N. sativa, followed by A. raddeana (0.2290) and A. coerulea (0.1222). Furthermore, the study identified 12 distinct hotspot regions characterized by elevated Pi values (> 0.1). These regions include trnH-GUG-psbA, matK-trnQ-UUG, psbK-trnR-UCU, atpF-atpI, rpoB-psbD, ycf3-ndhJ, ndhC-cemA, petA-psaJ, trnN-GUU-ndhF, trnV-GAC-rps12, ycf2-trnI-CAU, and ndhA-ycf1. Approximately, 24 tandem and 48 palindromic and forward repeats were detected in N. sativa plastome. The analysis revealed 32 microsatellites with the majority being mononucleotide repeats. In the N. sativa plastome, phenylalanine had the highest number of codons (1982 codons), while alanine was the least common amino acid with 260 codons. A phylogenetic tree, constructed using protein-coding genes, revealed a distinct monophyletic clade comprising N. sativa and N. damascene, closely aligned with the Cimicifugeae tribe and exhibiting robust support. This plastome provides valuable genetic information for precise species identification, phylogenetic resolution, and evolutionary studies of N. sativa.
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Affiliation(s)
- Lubna
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Ibrahim Khan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Science Research Center, University of Nizwa, 616, Nizwa, Oman.
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Zhang L, Zhang E, Wei Y, Zheng G. Phylogenetic analysis and divergence time estimation of Lycium species in China based on the chloroplast genomes. BMC Genomics 2024; 25:569. [PMID: 38844874 PMCID: PMC11155141 DOI: 10.1186/s12864-024-10487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Lycium is an economically and ecologically important genus of shrubs, consisting of approximately 70 species distributed worldwide, 15 of which are located in China. Despite the economic and ecological importance of Lycium, its phylogeny, interspecific relationships, and evolutionary history remain relatively unknown. In this study, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of 15 species, including subspecies, of the genus Lycium from China. RESULTS We sequenced and annotated 15 CPGs in this study. Comparative analysis of these genomes from these Lycium species revealed a typical quadripartite structure, with a total sequence length ranging from 154,890 to 155,677 base pairs (bp). The CPGs was highly conserved and moderately differentiated. Through annotation, we identified a total of 128-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the junctions of the IRb/LSC region were located in rps19 in all Lycium species, IRb/SSC between the ycf1 and ndhF genes, and SSC/IRa within the ycf1 gene. Sequence variation in the SSC region exceeded that in the IR region. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the 15 Lycium species. Comparative analyses revealed five hotspot regions in the CPG: trnR(UCU), atpF-atpH, ycf3-trnS(GGA), trnS(GGA), and trnL-UAG, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the 15 Lycium species formed a monophyletic group and were divided into two typical subbranches and three minor branches. Molecular dating suggested that Lycium diverged from its sister genus approximately 17.7 million years ago (Mya) and species diversification within the Lycium species of China primarily occurred during the recent Pliocene epoch. CONCLUSION The divergence time estimation presented in this study will facilitate future research on Lycium, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.
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Affiliation(s)
- Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Erdong Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Yuqing Wei
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, College of Biological Science & Engineering, National Ethnic Affairs Commission of the People's Republic of China, North Minzu University, Yinchuan, 750021, China
| | - Guoqi Zheng
- Key Laboratory of the Ministry of Education for Protection and Utilization of Special Biological Resources in the Western, School of Life Science, Ningxia University, Yinchuan, Ningxia, 750021, China.
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Wang Y, Wei Q, Xue T, He S, Fang J, Zeng C. Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high-throughput sequencing. BMC Genomics 2024; 25:561. [PMID: 38840044 PMCID: PMC11151499 DOI: 10.1186/s12864-024-10455-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Artemisia selengensis, classified within the genus Artemisia of the Asteraceae family, is a perennial herb recognized for its dual utility in culinary and medicinal domains. There are few studies on the chloroplast genome of A. selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult. RESULTS The chloroplast genomes of 10 A. selengensis in this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1 and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of A. selengensis' third codon position was A/T. The number of SSR repeats was 42-44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, 8 mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Artemisia Chrysanthemum and formed a monophyletic group with other Artemisia genera. CONCLUSIONS In this research, the present study systematically compared the chloroplast genomic features of A. selengensis and provided important information for the study of the chloroplast genome of A. selengensis and the evolutionary relationships among Asteraceae species.
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Affiliation(s)
- Yuhang Wang
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China
| | - Qingying Wei
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China
| | - Tianyuan Xue
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China
| | - Sixiao He
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China
| | - Jiao Fang
- School of Medicine, Jianghan University, Wuhan, Hubei, China
| | - Changli Zeng
- Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, School of Life Science, Jianghan University, Jianghan University, Wuhan, Hubei, China.
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Huang J, Hu X, Zhou Y, Peng YJ, Liu Z. Phylogeny, Genetic Diversity and Population Structure of Fritillaria cirrhosa and Its Relatives Based on Chloroplast Genome Data. Genes (Basel) 2024; 15:730. [PMID: 38927666 PMCID: PMC11202927 DOI: 10.3390/genes15060730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Fritillaria cirrhosa and its relatives have been utilized in traditional Chinese medicine for many years and are under priority protection in China. Despite their medicinal and protective value, research on their phylogeny, genetic diversity, and divergence remains limited. Here, we investigate the chloroplast genome variation architecture of 46 samples of F. cirrhosa and its relatives collected from various regions, encompassing the majority of wild populations across diverse geographical areas. The results indicate abundant variations in 46 accessions including 1659 single-nucleotide polymorphisms and 440 indels. Six variable markers (psbJ, ndhD, ycf1, ndhG, trnT-trnL, and rpl32-trnL) were identified. Phylogenetic and network analysis, population structure analysis, and principal component analysis showed that the 46 accessions formed five clades with significant divergence, which were related to their geographical distribution. The regions spanning from the southern Hengduan Mountains to the Qinghai-Tibet Plateau exhibited the highest levels of genetic diversity. F. cirrhosa and its relatives may have suffered a genetic bottleneck and have a relatively low genetic diversity level. Moreover, geographical barriers and discrete patches may have accelerated population divergence. The study offers novel perspectives on the phylogeny, genetic diversity, and population structure of F. cirrhosa and its relatives, information that can inform conservation and utilization strategies in the future.
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Affiliation(s)
- Jiao Huang
- College of Life Science, Leshan Normal University, Leshan 614000, China
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Conceição TA, Santos AS, Fernandes AKC, Meireles GN, de Oliveira FA, Barbosa RM, Gaiotto FA. Guiding seed movement: environmental heterogeneity drives genetic differentiation in Plathymenia reticulata, providing insights for restoration. AOB PLANTS 2024; 16:plae032. [PMID: 38883565 PMCID: PMC11176975 DOI: 10.1093/aobpla/plae032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/28/2024] [Indexed: 06/18/2024]
Abstract
Forest and landscape restoration is one of the main strategies for overcoming the environmental crisis. This activity is particularly relevant for biodiversity-rich areas threatened by deforestation, such as tropical forests. Efficient long-term restoration requires understanding the composition and genetic structure of native populations, as well as the factors that influence these genetic components. This is because these populations serve as the seed sources and, therefore, the gene reservoirs for areas under restoration. In the present study, we investigated the influence of environmental, climatic and spatial distance factors on the genetic patterns of Plathymenia reticulata, aiming to support seed translocation strategies for restoration areas. We collected plant samples from nine populations of P. reticulata in the state of Bahia, Brazil, located in areas of Atlantic Forest and Savanna, across four climatic types, and genotyped them using nine nuclear and three chloroplast microsatellite markers. The populations of P. reticulata evaluated generally showed low to moderate genotypic variability and low haplotypic diversity. The populations within the Savanna phytophysiognomy showed values above average for six of the eight evaluated genetic diversity parameters. Using this classification based on phytophysiognomy demonstrated a high predictive power for genetic differentiation in P. reticulata. Furthermore, the interplay of climate, soil and geographic distance influenced the spread of alleles across the landscape. Based on our findings, we propose seed translocation, taking into account the biome, with restricted use of seed sources acquired or collected from the same environment as the areas to be restored (Savanna or Atlantic Forest).
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Affiliation(s)
- Taise Almeida Conceição
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, USP, Piracicaba, São Paulo 13418-900, Brazil
| | - Alesandro Souza Santos
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Ane Karoline Campos Fernandes
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Gabriela Nascimento Meireles
- Laboratório de Marcadores Moleculares, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Fernanda Ancelmo de Oliveira
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, UNICAMP, Campinas, São Paulo 13083-875, Brazil
| | - Rafael Marani Barbosa
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Fernanda Amato Gaiotto
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, USP, Piracicaba, São Paulo 13418-900, Brazil
- Laboratório de Ecologia Aplicada à Conservação, Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, km 16, Ilhéus, Bahia 45662-900, Brazil
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11
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Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G. Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. BMC PLANT BIOLOGY 2024; 24:424. [PMID: 38764045 PMCID: PMC11103831 DOI: 10.1186/s12870-024-04999-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/08/2024] [Indexed: 05/21/2024]
Abstract
Rutaceae family comprises economically important plants due to their extensive applications in spices, food, oil, medicine, etc. The Rutaceae plants is able to better utilization through biotechnology. Modern biotechnological approaches primarily rely on the heterologous expression of functional proteins in different vectors. However, several proteins are difficult to express outside their native environment. The expression potential of functional genes in heterologous systems can be maximized by replacing the rare synonymous codons in the vector with preferred optimal codons of functional genes. Codon usage bias plays a critical role in biogenetic engineering-based research and development. In the current study, 727 coding sequences (CDSs) obtained from the chloroplast genomes of ten Rutaceae plant family members were analyzed for codon usage bias. The nucleotide composition analysis of codons showed that these codons were rich in A/T(U) bases and preferred A/T(U) endings. Analyses of neutrality plots, effective number of codons (ENC) plots, and correlations between ENC and codon adaptation index (CAI) were conducted, which revealed that natural selection is a major driving force for the Rutaceae plant family's codon usage bias, followed by base mutation. In the ENC vs. CAI plot, codon usage bias in the Rutaceae family had a negligible relationship with gene expression level. For each sample, we screened 12 codons as preferred and high-frequency codons simultaneously, of which GCU encoding Ala, UUA encoding Leu, and AGA encoding Arg were the most preferred codons. Taken together, our study unraveled the synonymous codon usage pattern in the Rutaceae family, providing valuable information for the genetic engineering of Rutaceae plant species in the future.
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Affiliation(s)
- Lianwen Shen
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, 650224, China
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China
- Guizhou Academy of Forestry, Guiyang, 550005, China
| | | | - Mei Liang
- Guizhou Province Forestry Science and Technology Extension Station, Guiyang, 550000, China
| | - Shang Qu
- Guizhou Academy of Forestry, Guiyang, 550005, China
| | - Shijing Feng
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
- Key Laboratory for Forest Genetics and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, 650224, China.
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, China.
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12
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Roestel JA, Wiersema JH, Jansen RK, Borsch T, Gruenstaeudl M. On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies. Cladistics 2024. [PMID: 38761095 DOI: 10.1111/cla.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024] Open
Abstract
The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.
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Affiliation(s)
- Jessica A Roestel
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - John H Wiersema
- Department of Botany, National Museum of Natural History - Smithsonian Institution, Washington, DC, 37012, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas Borsch
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
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Ye H, Wang Y, Liu H, Lei D, Li H, Gao Z, Feng X, Han M, Qie Q, Zhou H. The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1334. [PMID: 38794406 PMCID: PMC11125379 DOI: 10.3390/plants13101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.
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Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yiling Wang
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Dingfan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhimei Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaolong Feng
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Mian Han
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Qiyang Qie
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
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Wang Y, Zhao X, Chen Q, Yang J, Hu J, Jia D, Ma R. Complete Chloroplast Genome of Alternanthera sessilis and Comparative Analysis with Its Congeneric Invasive Weed Alternanthera philoxeroides. Genes (Basel) 2024; 15:544. [PMID: 38790173 PMCID: PMC11121667 DOI: 10.3390/genes15050544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Alternanthera sessilis is considered the closest relative to the invasive weed Alternanthera philoxeroides in China, making it an important native species for studying the invasive mechanisms and adaptations of A. philoxeroides. Chloroplasts play a crucial role in a plant's environmental adaptation, with their genomes being pivotal in the evolution and adaptation of both invasive and related species. However, the chloroplast genome of A. sessilis has remained unknown until now. In this study, we sequenced and assembled the complete chloroplast genome of A. sessilis using high-throughput sequencing. The A. sessilis chloroplast genome is 151,935 base pairs long, comprising two inverted repeat regions, a large single copy region, and a small single copy region. This chloroplast genome contains 128 genes, including 8 rRNA-coding genes, 37 tRNA-coding genes, 4 pseudogenes, and 83 protein-coding genes. When compared to the chloroplast genome of the invasive weed A. philoxeroides and other Amaranthaceae species, we observed significant variations in the ccsA, ycf1, and ycf2 regions in the A. sessilis chloroplast genome. Moreover, two genes, ccsA and accD, were found to be undergoing rapid evolution due to positive selection pressure. The phylogenetic trees were constructed for the Amaranthaceae family, estimating the time of independent species formation between A. philoxeroides and A. sessilis to be approximately 3.5186-8.8242 million years ago. These findings provide a foundation for understanding the population variation within invasive species among the Alternanthera genus.
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Affiliation(s)
- Yuanxin Wang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Xueying Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Qianhui Chen
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Jun Hu
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
| | - Dong Jia
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- Ministerial and Provincial Co-Innovation Centre for Endemic Crops Production with High-Quality and Effciency in Loess Plateau, Taigu 030801, China
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China; (Y.W.); (X.Z.); (Q.C.); (J.Y.); (J.H.)
- State Key Laboratory of Sustainable Dryland Agriculture (in Preparation), Shanxi Agricultural University, Taiyuan 030031, China
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15
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Coello AJ, Vargas P, Cano E, Riina R, Fernández-Mazuecos M. Phylogenetics and phylogeography of Euphorbia canariensis reveal an extreme Canarian-Asian disjunction but limited inter-island colonization. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:398-414. [PMID: 38444147 DOI: 10.1111/plb.13635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Euphorbia canariensis is an iconic endemic species representative of the lowland xerophytic communities of the Canary Islands. It is widely distributed in the archipelago despite having diasporas unspecialized for long-distance dispersal. Here, we reconstructed the evolutionary history of E. canariensis at two levels: a time-calibrated phylogenetic analysis aimed at clarifying interspecific relationships and large-scale biogeographic patterns; and a phylogeographic study focused on the history of colonization across the Canary Islands. For the phylogenetic study, we sequenced the ITS region for E. canariensis and related species of Euphorbia sect. Euphorbia. For the phylogeographic study, we sequenced two cpDNA regions for 28 populations representing the distribution range of E. canariensis. The number of inter-island colonization events was explored using PAICE, a recently developed method that includes a sample size correction. Additionally, we used species distribution modelling (SDM) to evaluate environmental suitability for E. canariensis through time. Phylogenetic results supported a close relationship between E. canariensis and certain Southeast Asian species (E. epiphylloides, E. lacei, E. sessiliflora). In the Canaries, E. canariensis displayed a west-to-east colonization pattern, not conforming to the "progression rule", i.e. the concordance between phylogeographic patterns and island emergence times. We estimated between 20 and 50 inter-island colonization events, all of them in the Quaternary, and SDM suggested a late Quaternary increase in environmental suitability for E. canariensis. The extreme biogeographic disjunction between Macaronesia and Southeast Asia (ca. 11,000 km) parallels that found in a few other genera (Pinus, Dracaena). We hypothesize that these disjunctions are better explained by extinction across north Africa and southwest Asia rather than long-distance dispersal. The relatively low number of inter-island colonization events across the Canaries is congruent with the low dispersal capabilities of E. canariensis.
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Affiliation(s)
- A J Coello
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - P Vargas
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - E Cano
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - R Riina
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - M Fernández-Mazuecos
- Departamento de Biología (Botánica), Universidad Autónoma de Madrid, Madrid, Spain
- Real Jardín Botánico (RJB), CSIC, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
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Kim TH, Ha YH, Setoguchi H, Choi K, Kim SC, Kim HJ. First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae). Genes (Basel) 2024; 15:380. [PMID: 38540439 PMCID: PMC10970243 DOI: 10.3390/genes15030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 06/14/2024] Open
Abstract
Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.
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Affiliation(s)
- Tae-Hee Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Kyung Choi
- Division of Garden and Plant Resources, Korea National Arboretum, Pocheon 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon 11186, Republic of Korea; (T.-H.K.)
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Tayebi Z, Moghaddam M, Mahmoodi M, Kazempour-Osaloo S. Evolutionary history of an Irano-Turanian cushion-forming legume (Onobrychis cornuta). BMC PLANT BIOLOGY 2024; 24:204. [PMID: 38509474 PMCID: PMC10953250 DOI: 10.1186/s12870-024-04895-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA (rpl32-trnL(UAG) and trnT(UGU)-trnL(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.
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Affiliation(s)
- Zahra Tayebi
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154
| | - Mahtab Moghaddam
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154
| | - Mohammad Mahmoodi
- Botany Research Division, Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 13185-116, Tehran, Iran
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran, 14115-154.
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Gaudeul M, Sweeney P, Munzinger J. An updated infrageneric classification of the pantropical species-rich genus Garcinia L. (Clusiaceae) and some insights into the systematics of New Caledonian species, based on molecular and morphological evidence. PHYTOKEYS 2024; 239:73-105. [PMID: 38523734 PMCID: PMC10960151 DOI: 10.3897/phytokeys.239.112563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/08/2024] [Indexed: 03/26/2024]
Abstract
Garcinia L. is a pantropically distributed genus comprised of at least 250 species of shrubs and trees and has centers of diversity located in Africa/Madagascar, Australasia, and Southeast Asia. The genus is notable due to its extreme diversity of floral form, common presence in lowland tropical rainforests worldwide, and potential pharmacological value. Across its entire geographic range, Garcinia lacks a recent taxonomic revision, with the last genus-level taxonomic treatment of Garcinia conducted over 40 years ago. In order to provide an evolutionary-based framework for a revised infrageneric classification of the genus and to investigate in more detail the systematics of New Caledonian species, we conducted molecular phylogenetic analyses using DNA sequence data for the nuclear ITS region on all samples, and for three chloroplast intergenic spacers (psbM-trnD, trnQ-rps16 and rps16-trnK) on a subset of our overall sampling. Our phylogenetic analyses are the most comprehensive to date for the genus, containing 111 biogeographically and morphologically diverse Garcinia species. The analyses support a broad circumscription of Garcinia, including several previously segregated genera (e.g. Allanblackia, Clusianthemum, Ochrocarpos p.p., Pentaphalangium, Rheedia, and Tripetalum). We recovered nine major clades falling within two major lineages, and we delimit 11 sections. We discuss each of the clades, assign them sectional names, discuss their distinguishing morphological features, compare our taxonomic treatment with the most recent sectional treatment, list representative species, note geographic distribution, and highlight some questions that deserve future investigations. We propose nine new nomenclatural combinations, four new names, and three new lectotypes. In New Caledonia (NC), a total of ten, all endemic, species are recognized and were included in our phylogenetic analyses, with several replicates per species (with the exception of G.virgata and G.urceolata, represented by a single accession each). New Caledonian species were retrieved within three separate clades, respectively including 1) G.balansae; 2) G.comptonii, G.neglecta, G.urceolata, G.virgata; and 3) G.amplexicaulis, G.densiflora, G.pedicellata, G.puat, G.vieillardii. Within NC, the phylogenies did not support the distinction between a putative undescribed species and G.balansae. However, it confirmed the distinction between NC species and both G.vitiensis (found in Fiji and Vanuatu) and G.adinantha (found in Fiji), suggesting that all NC species should be considered as endemics.
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Affiliation(s)
- Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceMuséum National d’Histoire Naturelle-CNRS-SU-EPHE-UAParisFrance
| | - Patrick Sweeney
- Yale Peabody Museum, Yale University, 170 Whitney Avenue, New Haven, CT 06511, USAYale UniversityNew HavenUnited States of America
| | - Jérôme Munzinger
- AMAP, University of Montpellier, IRD, INRAE, CIRAD, CNRS, Montpellier, FranceUniversity of MontpellierMontpellierFrance
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Park H, Park JH, Kang YJ. Characterization of the complete chloroplast genome of Wolffia arrhiza and comparative genomic analysis with relative Wolffia species. Sci Rep 2024; 14:5873. [PMID: 38467810 PMCID: PMC10928178 DOI: 10.1038/s41598-024-56394-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Lemnoideae, commonly referred to as the duckweed, are aquatic plants found worldwide. Wolffia species are known for their extreme reduction in size and complexity, lacking both roots and leaves, and they hold the distinction of being the smallest plants among angiosperms. Interestingly, it belongs to the Araceae family, despite its apparent morphological differences from land plants in the same family. Traditional morphological methods have limitations in classifying these plants, making molecular-level information essential. The chloroplast genome of Wolffia arrhiza is revealed that a total length of 169,602 bp and a total GC content of 35.78%. It follows the typical quadripartite structure, which includes a large single copy (LSC, 92,172 bp) region, a small single copy (SSC, 13,686 bp) region, and a pair of inverted repeat (IR, 31,872 bp each) regions. There are 131 genes characterized, comprising 86 Protein-Coding Genes, 37 Transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Moreover, 48 simple sequence repeats and 32 long repeat sequences were detected. Comparative analysis between W. arrhiza and six other Lemnoideae species identified 12 hotspots of high nucleotide diversity. In addition, a phylogenetic analysis was performed using 14 species belonging to the Araceae family and one external species as an outgroup. This analysis unveiled W. arrhiza and Wolffia globosa as closely related sister species. Therefore, this research has revealed the complete chloroplast genome data of W. arrhiza, offering a more detailed understanding of its evolutionary position and phylogenetic categorization within the Lemnoideae subfamily.
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Affiliation(s)
- Halim Park
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, 52828, Republic of Korea
| | | | - Yang Jae Kang
- Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Division of Life Science Department at Gyeongsang National University, Jinju, Republic of Korea.
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Huang YB, Qi ZC, Feng JY, Ge BJ, Huang CZ, Feng YQ, Wu J, Wei PR, Ito T, Kokubugata G, Li P, Wei YK. Salvia guidongensis sp. nov.: unraveling a critical evolutionary link in East Asian Salvia from Central China integrating morphology, phylogeny, and plastid genomics. FRONTIERS IN PLANT SCIENCE 2024; 15:1332443. [PMID: 38504896 PMCID: PMC10948445 DOI: 10.3389/fpls.2024.1332443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Introduction Salvia L., representing the largest genus within the mint family, is noted for its global distribution of approximately 1000 species, with East Asia, and particularly China, recognized as a critical center of diversity for the genus. Methods Our research was conducted through extensive fieldwork in Guidong County, Hunan Province, China, where we identified a previously undescribed species of Salvia. The identification process involved detailed morphological observations, phylogenetic analyses, and plastid genomics. Results The newly discovered species, Salvia guidongensis, exhibits unique characteristics not commonly observed in the East Asian lineage of Salvia, including dual floral colors within natural populations-either pale purple or pale yellow. Morphologically, while it shares similarities with members of sect. Glutinaria, S. guidongensis is distinct in its floral morphology, stature, and specific foliar traits. Phylogenetic analysis places S. guidongensis in a unique clade within the East Asian lineage of Salvia, suggesting it may serve as an important evolutionary link. Additionally, we explored the plastome features of S. guidongensis, comparing them with those of closely related species. Discussion The discovery of S. guidongensis not only entriches the taxonomic tapestry of Salvia but also provides critical insights into the biogeography and evolutionary pathways of the genus in East Asia. By integrating morphological and molecular data, we validate the novel status of S. guidongensis and highlight its significance in bridging taxonomic and evolutionary gaps within Sect. Glutinaria of Salvia.
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Affiliation(s)
- Yan-Bo Huang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Zhe-Chen Qi
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jie-Ying Feng
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bin-Jie Ge
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | | | - Yu-Qing Feng
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jing Wu
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pu-Rui Wei
- East China Survey and Planning Institute of the National Forestry and Grassland Administration, Hangzhou, China
| | - Takuro Ito
- Tohoku University Botanical Gardens, 12-2 Kawauchi, Aoba-ku, Sendai-shi, Miyagi, Japan
| | - Goro Kokubugata
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Kun Wei
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- Shanghai Engineering Research Centre of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai, China
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Yu Q, Hu J, Hu X, Zhou Y, Wang F, Jiang S, Wang Y. Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes. FRONTIERS IN PLANT SCIENCE 2024; 15:1345624. [PMID: 38450397 PMCID: PMC10915042 DOI: 10.3389/fpls.2024.1345624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.
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Affiliation(s)
- Qiushi Yu
- Xinglongshan Forest Ecosystem National Positioning Observation and Research Station, Gansu Research Academy of Forestry Science and Technology, Lanzhou, China
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - Jing Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Xiaoke Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yongfeng Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fanglin Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Shengxiu Jiang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yuqi Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
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Li Z, Duan B, Zhou Z, Fang H, Yang M, Xia C, Zhou Y, Wang J. Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing. BMC Genomics 2024; 25:39. [PMID: 38191291 PMCID: PMC10773089 DOI: 10.1186/s12864-023-09920-2] [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: 08/02/2023] [Accepted: 12/17/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Scutellaria baicalensis Georgi has been extensively used as a medicinal herb in China for over 2000 years. They may be intentionally or inadvertently substituted or blended with comparable species in the local market, threatening clinical medication safety. Molecular markers are effective tools to prevent misidentification and eliminate doping and falsification among Scutellaria plants. This study screened four highly variable regions to identify Scutellaria and its adulterants. In addition, a phylogenetic analysis was performed using the complete cp genome combined with published Scutellaria species samples. Moreover, a comparative analysis of the cp genomes was conducted to investigate the cp genome evolution of S. baicalensis. RESULTS The complete cp genome of five species of Scutellaria was sequenced for the first time, and four previously published Scutellaria species were re-sequenced. They all exhibited a conserved quadripartite structure in their cp genomes, including two distinct regions, namely a small and large single copy region, respectively, and two inverted repeats encompassing the majority of ribosomal RNA genes. Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. Four highly variable regions (matK-rps16, ndhC-trnV-UAC, psbE-petL, and rps16-trnQ-UUG) may function as potential molecular markers for differentiating S. baicalensis from its adulterants. Additionally, the monophyly of Scutellaria was ascertained and could be reclassified into two subgenera, subgenus Anaspis and subgenus Scutellaria, as evidenced by the phylogenetic analyses on sequences of cp genome and shared protein-coding sequences. According to the molecular clock analysis, it has been inferred that the divergence of Scutellaria occurred at approximately 4.0 Mya during the Pliocene Epoch. CONCLUSION Our study provides an invaluable theoretical basis for further Scutellaria species identification, phylogenetics, and evolution analysis.
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Affiliation(s)
- Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University, Yanji, 133002, China
| | - Hui Fang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, 671000, China
| | - Ying Zhou
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- Institute of Caulis Dendrobii of Longling County, Baoshan, 678300, China.
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, 671000, China.
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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Choudhary A, Shekhawat D, Pathania J, Sita K, Sharma S, Chawla A, Jaiswal V. Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya. Mol Biol Rep 2024; 51:75. [PMID: 38175298 DOI: 10.1007/s11033-023-08927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species. METHODS AND RESULTS A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution. CONCLUSION ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.
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Affiliation(s)
- Anita Choudhary
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Shekhawat
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Jyotsna Pathania
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kumari Sita
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shailika Sharma
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Amit Chawla
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Vandana Jaiswal
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Zhang SY, Yan HF, Wei L, Liu TJ, Chen L, Hao G, Wu X, Zhang QL. Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae). BMC PLANT BIOLOGY 2024; 24:23. [PMID: 38166728 PMCID: PMC10763413 DOI: 10.1186/s12870-023-04697-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. RESULTS In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113-114 genes, including 78-79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30 Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. CONCLUSIONS The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus.
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Affiliation(s)
- Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Qiao-Ling Zhang
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, China.
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Huang G, Li L, Wang X, Yang L, Wang Y, Wu D, Wu J. The complete plastid genome of Rhamnus leptacantha Schneid. (Rhamnaceae). Mitochondrial DNA B Resour 2024; 9:33-36. [PMID: 38187011 PMCID: PMC10769139 DOI: 10.1080/23802359.2023.2300468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
Rhamnus leptacantha C.K.Schneid. (1914). is a rare shrub species of the genus Rhamnus. The complete plastid genome of Rhamnus leptacantha was sequenced for the first time in this study. The total length of this genome is 161,248 bp with a large single copy (LSC) region (89,386 bp), a small single copy (SSC) region (19,000 bp), and two inverted repeat regions (IRs, 26,431 bp). A total of 133 functional genes were annotated, including 88 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Plastome of R. leptacantha displayed a conservative structure and gene order. Phylogenetic analysis strongly supported R. leptacantha clustered with other members of genus Rhamnus. This study provides a foundation for further investigation of the complete chloroplast genome in inferring the evolution within the Rhamnaceae family.
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Affiliation(s)
- Guiyun Huang
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
| | - Linbao Li
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
| | - Xiongying Wang
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
| | - Lanfang Yang
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
| | - Yeqing Wang
- Hubei Wufeng Houhe National Nature Reserve Administration Science Research Institute, Yichang, Hubei, China
| | - Di Wu
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
| | - Jinhua Wu
- Yangtze River Biodiversity Center, Yangtze River Ecological Environment Engineering Research Center, China Three Gorges Corporation Ltd, Yichang, Hubei, China
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Serrano M, Ortiz S. Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization. PLANTS (BASEL, SWITZERLAND) 2023; 12:4176. [PMID: 38140501 PMCID: PMC10747609 DOI: 10.3390/plants12244176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Groups with morphological stasis are an interesting framework to address putative cryptic species that may be hidden behind traditional taxonomic treatments, particularly when distribution ranges suggest disjunct and environmentally heterogeneous biogeographic patterns. New hypotheses of delimitation of evolutionary independent units can lead to the identification of different biogeographic processes, laying the foundation to investigate their historical and ecological significance. Jasione is a plant genus with a distribution centered in the Mediterranean basin, characterized by significant morphological stasis. Within the western Mediterranean J. gr. crispa species complex, J. sessiliflora s.l. and allied taxa form a distinct group, occupying environmentally diverse regions. At least two ploidy levels, diploid and tetraploid, are known to occur in the group. The internal variability is assessed with phylogenetic tools, viz. GMYC and ASAP, for species delimitation. The results are compared with other lines of evidence, including morphology and cytology. The fitting of distribution patterns of the inferred entities to chorological subprovinces is also used as a biogeographical and environmental framework to test the species hypothesis. Despite the scarcity of diagnostic morphological characters in the group, phylogenetic delimitation supports the description of at least one cryptic species, a narrow endemic in the NE Iberian Peninsula. Moreover, the results support the segregation of a thermophilic group of populations in eastern Iberia from J. sessiliflora. Ploidy variation from a wide geographical survey supports the systematic rearrangement suggested by species delimitation. Taxonomic reorganization in J. sessiliflora s.l. would allow ecological interpretations of distribution patterns in great accordance with biogeographical regionalization at the subprovince level, supporting geobotanical boundaries as a framework to interpret species ecological coherence of cryptic lineages. These results suggest that species differentiation, together with geographic isolation and polyploidization, is associated with adaptation to different environments, shifting from more to less thermophilic conditions. Thus, the recognition of concealed evolutionary entities is essential to correctly interpret biogeographical patterns in regions with a complex geologic and evolutionary history, such as the Mediterranean basin, and biogeographical units emerge as biologically sound frameworks to test the species hypothesis.
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Affiliation(s)
- Miguel Serrano
- Department of Botany, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
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Xiao Y, Wang X, He Z, Lv Y, Zhang C, Hu X. Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes. Ecol Evol 2023; 13:e10828. [PMID: 38094154 PMCID: PMC10716671 DOI: 10.1002/ece3.10828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 07/03/2024] Open
Abstract
Toona ciliata is an endangered species due to over-cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well-mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL-trnF) and showed that genetic differentiation was generally insignificant among varieties (Ф st = 0%-5%). Purifying selection occurred in all protein-coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein-coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome-based phylogeny did not support the morphology-based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.
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Affiliation(s)
- Yu Xiao
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Xi Wang
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Zi‐Han He
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Yan‐Wen Lv
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
| | - Chun‐Hua Zhang
- Institute of Highland Forest Science, Chinese Academy of ForestryKunmingChina
| | - Xin‐Sheng Hu
- College of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmGuangzhouChina
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Hu L, Lu T, Wang X, Wang J, Shi W. Conservation Priorities and Demographic History of Saussurea involucrata in the Tianshan Mountains and Altai Mountains. Life (Basel) 2023; 13:2209. [PMID: 38004349 PMCID: PMC10672382 DOI: 10.3390/life13112209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Rare and vulnerable endemic plants represent different evolutionary units that occur at different times, and protecting these species is a key issue in biological protection. Understanding the impact of the history of endangered plant populations on their genetic diversity helps to reveal evolutionary history and is crucial for guiding conservation efforts. Saussurea involucrata, a perennial alpine species mainly distributed in the Tianshan Mountains, is famous for its medicinal value but has become endangered due to over-exploitation. In the present study, we employed both nuclear and chloroplast DNA sequences to investigate the genetic distribution pattern and evolutionary history of S. involucrata. A total of 270 individuals covering nine S. involucrata populations were sampled for the amplification and sequencing of nrDNA Internal Transcribed Spacer (ITS) and chloroplast trnL-trnF, matK and ndhF-rpl32 sequences. Via calculation, we identified 7 nuclear and 12 plastid haplotypes. Among the nine populations, GL and BA were characterized by high haplotype diversity, whereas BG revealed the lowest haplotype diversity. Molecular dating estimations suggest that divergence among S. involucrata populations occurred around 0.75 Ma, coinciding with the uplift of Tianshan Mountains. Our results reveal that both isolation-by-distance (IBD) and isolation-by-resistance (IBR) have promoted genetic differentiation among populations of S. involucrata. The results from the ecological niche modeling analyses show a more suitable habitat for S. involucrata in the past than at present, indicating a historical distribution contraction of the species. This study provides new insight into understanding the genetic differentiation of S. involucrata, as well as the theoretical basis for conserving this species.
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Affiliation(s)
- Lin Hu
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (L.H.); (X.W.)
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830011, China;
| | - Ting Lu
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830011, China;
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (L.H.); (X.W.)
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (L.H.); (X.W.)
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (L.H.); (X.W.)
- Turpan Eremophytes Botanic Garden, The Chinese Academy of Sciences, Turpan 838008, China
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29
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Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
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Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
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Martínez-Gómez J, Park S, Hartogs SR, Soza VL, Park SJ, Di Stilio VS. Flower morphology as a predictor of pollination mode in a biotic to abiotic pollination continuum. ANNALS OF BOTANY 2023; 132:61-76. [PMID: 37235981 PMCID: PMC10550269 DOI: 10.1093/aob/mcad069] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS Wind pollination has evolved repeatedly in flowering plants, yet the identification of a wind pollination syndrome as a set of integrated floral traits can be elusive. Thalictrum (Ranunculaceae) comprises temperate perennial herbs that have transitioned repeatedly from insect to wind pollination while also exhibiting mixed pollination, providing an ideal system to test for evolutionary correlation between floral morphology and pollination mode in a biotic to abiotic continuum. Moreover, the lack of floral organ fusion across this genus allows testing for specialization to pollination vectors in the absence of this feature. METHODS We expanded phylogenetic sampling in the genus from a previous study using six chloroplast loci, which allowed us to test whether species cluster into distinct pollination syndromes based on floral morphology. We then used multivariate analyses on floral traits followed by ancestral state reconstruction of the emerging flower morphotypes and determined whether these traits are evolutionarily correlated under a Bayesian framework with Brownian motion. KEY RESULTS Floral traits fell into five distinct clusters, which were reduced to three after considering phylogenetic relatedness and were largely consistent with flower morphotypes and associated pollination vectors. Multivariate evolutionary analyses found a positive correlation between the lengths of floral reproductive structures (styles, stigmas, filaments and anthers). Shorter reproductive structures tracked insect-pollinated species and clades in the phylogeny, whereas longer structures tracked wind-pollinated ones, consistent with selective pressures exerted by biotic vs. abiotic pollination vectors, respectively. CONCLUSIONS Although detectable suites of integrated floral traits across Thalictrum were correlated with wind or insect pollination at the extremes of the morphospace distribution, a presumed intermediate, mixed pollination mode morphospace was also detected. Thus, our data broadly support the existence of detectable flower morphotypes from convergent evolution underlying the evolution of pollination mode in Thalictrum, presumably via different paths from an ancestral mixed pollination state.
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Affiliation(s)
- Jesús Martínez-Gómez
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Samantha R Hartogs
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA
| | - Valerie L Soza
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA
| | - Seon Joo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - Verónica S Di Stilio
- Department of Biology, University of Washington, PO Box 351800, Seattle, WA 98195, USA
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Rose JP, Wiese J, Pauley N, Dirmenci T, Celep F, Xiang CL, Drew BT. East Asian-North American disjunctions and phylogenetic relationships within subtribe Nepetinae (Lamiaceae). Mol Phylogenet Evol 2023; 187:107873. [PMID: 37429334 DOI: 10.1016/j.ympev.2023.107873] [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: 08/05/2022] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
Biogeographic disjunctions, including intercontinental disjunctions, are frequent across plant lineages and have been of considerable interest to biologists for centuries. Their study has been reinvigorated by molecular dating and associated comparative methods. One of the "classic" disjunction patterns is that between Eastern Asia and North America. It has been speculated that this pattern is the result of vicariance following the sundering of a widespread Acrto-Teritary flora. Subtribe Nepetinae in the mint family (Lamiaceae) is noteworthy because it contains three genera with this disjunction pattern: Agastache, Dracocephalum, and Meehania. These disjunctions are ostensibly the result of three separate events, allowing for concurrent testing of the tempo, origin, and type of each biogeographic event. Using four plastid and four nuclear markers, we estimated divergence times and analyzed the historical biogeography of Nepetinae, including comprehensive sampling of all major clades for the first time. We recover a well-supported and largely congruent phylogeny of Nepetinae between genomic compartments, although several cases of cyto-nuclear discordance are evident. We demonstrate that the three disjunctions are pseudo-congruent, with unidirectional movement from East Asia at slightly staggered times during the late Miocene and early Pliocene. With the possible exception of Meehania, we find that vicariance is likely the underlying driver of these disjunctions. The biogeographic history of Meehania in North America may be best explained by long-distance dispersal, but a more complete picture awaits deeper sampling of the nuclear genome and more advanced biogeographical models.
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Affiliation(s)
- Jeffrey P Rose
- Department of Biology, University of Nebraska-Kearney, NE, Kearney, 68849, USA
| | - Joshua Wiese
- Department of Biology, University of Nebraska-Kearney, NE, Kearney, 68849, USA; Platte River Whooping Crane Maintenance Trust, Wood River, NE, 68883, USA
| | - Nicole Pauley
- Department of Biology, University of Nebraska-Kearney, NE, Kearney, 68849, USA; U.S. Fish and Wildlife Service, Maine Ecological Services Field Office, Orland, ME, 04431, USA
| | - Tuncay Dirmenci
- Balıkesir University, Department of Biology Education, Merkez Balikesir, Turkey; Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AB, UK
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and Sciences, Kirikkale University, Kirikkale, Turkey
| | - Chun-Lei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, NE, Kearney, 68849, USA.
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Gajdošová Z, Svitok M, Cetlová V, Mártonfiová L, Kučera J, Kolarčik V, Hurdu BI, Sîrbu IM, Turisová I, Turis P, Slovák M. Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae). AOB PLANTS 2023; 15:plad056. [PMID: 37899980 PMCID: PMC10601019 DOI: 10.1093/aobpla/plad056] [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: 02/13/2023] [Accepted: 08/09/2023] [Indexed: 10/31/2023]
Abstract
Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.
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Affiliation(s)
- Zuzana Gajdošová
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Marek Svitok
- Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Ul. T. G. Masaryka 24, SK-960 01 Zvolen, Slovak Republic
- Department of Forest Ecology, Czech University of Life Sciences Prague, CZ-16 521 Suchdol, Praha 6, Czech Republic
| | - Veronika Cetlová
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Lenka Mártonfiová
- Botanical Garden of Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-043 52 Košice, Slovak Republic
| | - Jaromír Kučera
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-041 54 Košice, Slovak Republic
| | - Bogdan-Iuliu Hurdu
- Department of Taxonomy and Evolution, Institute of Biological Research, 48 Republicii St., R-400015 Cluj-Napoca, Romania
| | - Ioana-Minodora Sîrbu
- Faculty of Biology, University of Bucharest, Splaiul Independenței 91–95, R-050095Bucharest, Romania
| | - Ingrid Turisová
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Tajovského 40, SK-974 01 Banská Bystrica, Slovak Republic
| | - Peter Turis
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University in Banská Bystrica, Tajovského 40, SK-974 01 Banská Bystrica, Slovak Republic
| | - Marek Slovák
- Department of Evolution and Systematics, Institute of Botany, Plant Sciences and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 23 Bratislava, Slovak Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha, Czech Republic
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Kirschner P, Záveská E, Hülber K, Wessely J, Willner W, Schönswetter P, Frajman B. Evolutionary dynamics of Euphorbia carniolica suggest a complex Plio-Pleistocene history of understorey species of deciduous forest in southeastern Europe. Mol Ecol 2023; 32:5350-5368. [PMID: 37632417 PMCID: PMC10946815 DOI: 10.1111/mec.17102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 08/28/2023]
Abstract
Deciduous forests form the dominant natural vegetation of Europe today, but were restricted to small refugia during Pleistocene cold stages, implying an evolutionary past shaped by recurrent range contractions and expansions. Cold-stage forest refugia were probably widespread in southern and central Europe, with the northwestern Balkan Peninsula being of particular importance. However, the actual number and location of deciduous forest refugia, as well as the connections between them, remain disputed. Here, we address the evolutionary dynamics of the deciduous forest understorey species Euphorbia carniolica as a proxy for past forest dynamics. To do so, we obtained genomic and morphometric data from populations representing the species' entire range, investigated phylogenetic position and intraspecific genetic variation, tested explicit demographic scenarios and applied species distribution models. Our data support two disjoint groups linked to separate refugia on the northwestern and central Balkan Peninsula. We find that genetic differentiation between groups started in the early Pleistocene via vicariance, suggesting a larger distribution in the past. Both refugia acted as sources for founder events to the southeastern Alps and the Carpathians; the latter were likely colonised before the last cold stage. In line with traditional views on the pre-Pleistocene origin of many southeastern European deciduous forest species, the origin of E. carniolica was dated to the late Pliocene. The fact that E. carniolica evolved at a time when a period of continuous forestation was ending in much of Eurasia provides an interesting biogeographical perspective on the past links between Eurasian deciduous forests and their biota.
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Affiliation(s)
- Philipp Kirschner
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Faculty of Agricultural, Environmental and Food SciencesFree University of Bozen‐BolzanoBolzanoItaly
| | - Eliška Záveská
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Karl Hülber
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Johannes Wessely
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Wolfgang Willner
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | | | - Božo Frajman
- Department of BotanyUniversity of InnsbruckInnsbruckAustria
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Hu HS, Mao JY, Wang X, Liang YZ, Jiang B, Zhang DQ. Plastid phylogenomics and species discrimination in the "Chinese" clade of Roscoea (Zingiberaceae). PLANT DIVERSITY 2023; 45:523-534. [PMID: 37936815 PMCID: PMC10625918 DOI: 10.1016/j.pld.2023.03.012] [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] [Received: 11/21/2022] [Revised: 03/15/2023] [Accepted: 03/30/2023] [Indexed: 11/09/2023]
Abstract
Roscoea is an alpine or subalpine genus from the pan-tropical family Zingiberaceae, which consists of two disjunct groups in geography, namely the "Chinese" clade and the "Himalayan" clade. Despite extensive research on the genus, Roscoea species remain poorly defined and relationships between these species are not well resolved. In this study, we used plastid genomes of nine species and one variety to resolve phylogenetic relationships within the "Chinese" clade of Roscoea and as DNA super barcodes for species discrimination. We found that Roscoea plastid genomes ranged in length from 163,063 to 163,796 bp, and encoded 113 genes, including 79 protein-coding genes, 30 tRNA genes, four rRNA genes. In addition, expansion and contraction of the IR regions showed obvious infraspecific conservatism and interspecific differentiation. Plastid phylogenomics revealed that species belonging to the "Chinese" clade of Roscoea can be divided into four distinct subclades. Furthermore, our analysis supported the independence of R. cautleoides var. pubescens, the recovery of Roscoea pubescens Z.Y. Zhu, and a close relationship between R. humeana and R. cautloides. When we used the plastid genome as a super barcode, we found that it possessed strong discriminatory power (90%) with high support values. Intergenic regions provided similar resolution, which was much better than that of protein-coding regions, hypervariable regions, and DNA universal barcodes. However, plastid genomes could not completely resolve Roscoea phylogeny or definitively discriminate species. These limitations are likely related to the complex history of Roscoea speciation, poorly defined species within the genus, and the maternal inheritance of plastid genomes.
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Affiliation(s)
- Hai-Su Hu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Jiu-Yang Mao
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Yu-Ze Liang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
| | - Bei Jiang
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
| | - De-Quan Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, China
- College of Pharmacy, Dali University, Dali 671000, Yunnan, China
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali 671000, Yunnan, China
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Cai H, Ren Y, Du J, Liu L, Long L, Yang M. Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species. Int J Mol Sci 2023; 24:12954. [PMID: 37629135 PMCID: PMC10454583 DOI: 10.3390/ijms241612954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis showed that the Deutzia species had 41-45 scattered repeats and 199-201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29-31 RNA editing events and 163-194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.
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Affiliation(s)
- Hongyu Cai
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Yachao Ren
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Juan Du
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Shijiazhuang Botanical Garden, Shijiazhuang 050299, China
| | - Lingyun Liu
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Lianxiang Long
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
| | - Minsheng Yang
- Forestry College, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071055, China
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Zhou J, Niu J, Wang X, Yue J, Zhou S, Liu Z. Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses. BMC PLANT BIOLOGY 2023; 23:368. [PMID: 37488499 PMCID: PMC10367252 DOI: 10.1186/s12870-023-04376-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. RESULTS The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. CONCLUSIONS The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.
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Affiliation(s)
- Jing Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Junmei Niu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Xinyue Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Jiarui Yue
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Shilin Zhou
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, China
| | - Zhenwen Liu
- Yunnan Academy of Forestry and Grassland, Kunming, China.
- Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province, Kunming, China.
- Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming, China.
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Osmonali BB, Vesselova PV, Kudabayeva GM, Skaptsov MV, Shmakov AI, Friesen N. Phylogeny and Flow Cytometry of the Genus Kalidium Moq. (Amaranthaceae s.l.) in Kazakhstan. PLANTS (BASEL, SWITZERLAND) 2023; 12:2619. [PMID: 37514234 PMCID: PMC10383796 DOI: 10.3390/plants12142619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023]
Abstract
The article presents data on phylogeny, genome size, and ploidy of species of the genus Kalidium Moq. in the flora of Kazakhstan. Genus Kalidium belongs to the tribe Salicornieae of the subfamily Salicornioideae of the family Chenopodiaceae and unites eight species, the main range of which covers the Iranian-Turanian and Central Asian deserts. There are four species in the flora of Kazakhstan: K. foliatum, K. caspicum, K. schrenkianum, and the recently described K. juniperinum. Populations of species of the genus Kalidium in the saline deserts of Kazakhstan occupy large areas, often forming monodominant communities. Sometimes there is a joint growth of two and very rarely three species of the genus. During the period of fieldwork (2021-2022), populations were identified in which these species grew together with a predominance, in most cases, of K. caspicum. Samples of representatives from 15 populations were collected for research. Selected plant samples were studied by flow cytometry to determine plant ploidy. Sequencing of nrITS and two chloroplast fragments were used to build a phylogenetic tree, including sequences from the NCBI database., A phylogenetic tree of species of the genus Kalidium was compiled, which takes previously published data into consideration. In the valley of the middle reaches of the Syrdarya River, tetraploid populations of K. caspicum were found. A hybrid between K. foliatum and K. caspicum was found in the Ili River valley (Almaty region, Uigur district). To identify phylogenetic processes at the intraspecific level, the SCoT (Start codon targeted) fingerprinting method was used.
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Affiliation(s)
- B B Osmonali
- Institute of Botany and Phytointroduction, Almaty 050040, Kazakhstan
- Department of Biodiversity and Bioresources, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - P V Vesselova
- Institute of Botany and Phytointroduction, Almaty 050040, Kazakhstan
| | - G M Kudabayeva
- Institute of Botany and Phytointroduction, Almaty 050040, Kazakhstan
| | - M V Skaptsov
- South Siberian Botanical Garden, Faculty of Biology, Altai State University, Barnaul 656906, Russia
| | - A I Shmakov
- South Siberian Botanical Garden, Faculty of Biology, Altai State University, Barnaul 656906, Russia
| | - N Friesen
- Botanical Garden, School of Biology/Chemistry, Osnabruck University, 49076 Osnabruck, Germany
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Zhang Z, Mu W, Kong W, Liu J, Zhao J, Zhao Q, Shi M, Zhao H, Liu J, Shi L. Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients. PLoS One 2023; 18:e0286069. [PMID: 37399206 DOI: 10.1371/journal.pone.0286069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/08/2023] [Indexed: 07/05/2023] Open
Abstract
Identifying plant, fungal, and animal ingredients in a specific mixture remains challenging during the limitation of PCR amplification and low specificity of traditional methods. Genomic DNA was extracted from mock and pharmaceutical samples. Four type of DNA barcodes were generated from shotgun sequencing dataset with the help of a local bioinformatic pipeline. Taxa of each barcode was assigned by blast to TCM-BOL, BOLD, and GenBank. Traditional methods including microscopy, thin layer chromatography (TLC), and high-performance liquid chromatography (HPLC) were carried out according to Chinese pharmacopoeia. On average, 6.8 Gb shotgun reads were sequenced from genomic DNA of each sample. Then, 97, 11, 10, 14, and one operational taxonomic unit (OTU) were generated for ITS2, psbA-trnH, rbcL, matK, and COI, respectively. All the labeled ingredients including eight plant, one fungal, and one animal species were successfully detected in both the mock and pharmaceutical samples, in which Chebulae Fructus, Poria, and Fritilariae Thunbergia Bulbus were identified via mapping reads to organelle genomes. In addition, four unlabeled plant species were detected from pharmaceutical samples, while 30 genera of fungi, such as Schwanniomyces, Diaporthe, Fusarium were detected from mock and pharmaceutical samples. Furthermore, the microscopic, TLC, and HPLC analysis were all in accordance with the standards stipulated by Chinese Pharmacopoeia. This study indicated that shotgun metabarcoding could simultaneously identified plant, fungal, and animal ingredients in herbal products, which has the ability to serve as a valuable complement to traditional methods.
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Affiliation(s)
- Zhaolei Zhang
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiali Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingyi Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Hongye Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Huang Y, Ma Q, Sun J, Zhou L, Lai C, Li P, Jin X, Zhang Y. Comparative analysis of Diospyros (Ebenaceae) plastomes: Insights into genomic features, mutational hotspots, and adaptive evolution. Ecol Evol 2023; 13:e10301. [PMID: 37456073 PMCID: PMC10338900 DOI: 10.1002/ece3.10301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 06/17/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
Diospyros (Ebenaceae) is a widely distributed genus of trees and shrubs from pantropical to temperate regions, with numerous species valued for their fruits (persimmons), timber, and medicinal values. However, information regarding their plastomes and chloroplast evolution is scarce. The present study performed comparative genomic and evolutionary analyses on plastomes of 45 accepted Diospyros species, including three newly sequenced ones. Our study showed a highly conserved genomic structure across the Diospyros species, with 135-136 encoding genes, including 89 protein-coding genes, 1-2 pseudogenes (Ψycf1 for all, Ψrps19 for a few), 37 tRNA genes and 8 rRNA genes. Comparative analysis of Diospyros identified three intergenic regions (ccsA-ndhD, rps16-psbK and petA-psbJ) and five genes (rpl33, rpl22, petL, psaC and rps15) as the mutational hotspots in these species. Phylogenomic analysis identified the phylogenetic position of three newly sequenced ones and well supported a monophylogenetic (sub)temperate taxa and four clades in the pantropical taxa. The analysis codon usage identified 30 codons with relative synonymous codon usage (RSCU) values >1 and 29 codons ending with A and U bases. A total of three codons (UUA, GCU, and AGA) with highest RSCU values were identified as the optimal codons. Effective number of codons (ENC)-plot indicated the significant role of mutational pressure in shaping codon usage, while most protein-coding genes in Diospyros experienced relaxed purifying selection (d N/d S < 1). Additionally, the psbH gene showed positive selection (d N/d S > 1) in the (sub)temperate species. Thus, the results provide a meaningful foundation for further elaborating Diospyros's genetic architecture and taxonomy, enriching genetic diversity and conserving genetic resources.
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Affiliation(s)
- Yue Huang
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
| | - Qing Ma
- College of Biology and Environmental EngineeringZhejiang Shuren UniversityHangzhouChina
| | - Jing Sun
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
| | - Li‐Na Zhou
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
| | - Chan‐Juan Lai
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life SciencesZhejiang UniversityHangzhouChina
| | - Xin‐Jie Jin
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
| | - Yong‐Hua Zhang
- College of Life and Environmental ScienceWenzhou UniversityWenzhouChina
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Vitales D, Guerrero C, Garnatje T, Romeiras MM, Santos A, Fernandes F, Vallès J. Parallel anagenetic patterns in endemic Artemisia species from three Macaronesian archipelagos. AOB PLANTS 2023; 15:plad057. [PMID: 37649982 PMCID: PMC10465267 DOI: 10.1093/aobpla/plad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023]
Abstract
Anagenetic speciation is an important mode of evolution in oceanic islands, yet relatively understudied compared to adaptive radiation. In the Macaronesian region, three closely related species of Artemisia (i.e. A. argentea, A. thuscula and A. gorgonum) are each endemic from a single archipelago (i.e. Madeira, Canary Islands and Cape Verde, respectively), representing a perfect opportunity to study three similar but independent anagenetic speciation processes. By analysing plastid and nuclear DNA sequences, as well as nuclear DNA amount data, generated from a comprehensive sampling in all the islands and archipelagos where these species are currently distributed, we intend to find common evolutionary patterns that help us explain the limited taxonomic diversification experienced by endemic Macaronesian Artemisia. Our time-calibrated phylogenetic reconstruction suggested that divergence among the three lineages occurred in a coincidental short period of time during the Pleistocene. Haplotype and genetic differentiation analyses showed similar diversity values among A. argentea, A. thuscula and A. gorgonum. Clear phylogeographic patterns-showing comparable genetic structuring among groups of islands-were also found within the three archipelagos. Even from the cytogenetic point of view, the three species presented similarly lower genome size values compared to the mainland closely related species A. arborescens. We hypothesize that the limited speciation experienced by the endemic Artemisia in Madeira, Canary Islands and Cape Verde archipelagos could be related to their recent parallel evolutionary histories as independent lineages, combined with certain shared characteristics of seed dispersal, pollen transport and type of habitat.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Carmen Guerrero
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
| | - Maria M Romeiras
- LEAF—Linking Landscape, Environment, Agriculture and Food Research Center & Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1340-017 Lisboa, Portugal
| | - Arnoldo Santos
- Calle Guaidil 16, 38280 Tegueste, Tenerife, Islas Canarias, Spain
| | - Francisco Fernandes
- Jardim Botânico da Madeira Eng. Rui Vieira, Caminho do Meio Bom Sucesso, Madeira, Portugal
| | - Joan Vallès
- Laboratori de Botànica (UB), Unitat Associada al CSIC, Facultat de Farmàcia i Ciències de l’Alimentació-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
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41
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Ro N, Haile M, Ko HC, Cho GT, Lee J, Kim B, Lee S, Kim SH. Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm. Genes (Basel) 2023; 14:1315. [PMID: 37510220 PMCID: PMC10379237 DOI: 10.3390/genes14071315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The phenolic compounds in eggplant offer potential natural antioxidants for improved health. A large number of samples were examined in order to find eggplant germplasm with a high potential for health promotion. A genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNPs) associated with variations in total phenolic content (TPC) and antioxidant activity in eggplants, including ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) scavenging activity and ferric reducing antioxidant power (FRAP). TPC values varied from 14.19 to 842.90 mg gallic acid equivalent (GAE)/100 g of dry weight of eggplant fruit powder. TPC showed a strong positive correlation with both FRAP and ABTS (r = 0.89 *** and 0.77 ***, respectively). The GWAS identified 20 SNPs that were significantly associated out of 29,183 SNPs. Out of the 20 significant SNPs, 11 showed associations with TPC, 4 with ABTS activity, and 5 with FRAP. Among the SNPs associated with TPC, one SNP was found on each of Chromosomes 3, 4, 7, and 12. In contrast, Chromosome 5 comprised two SNPs associated to TPC. Furthermore, the gene encoding IRX12 laccase-4 on Chromosome 10 was found to contain five SNPs associated with TPC. Four significantly linked SNPs on Chromosomes 1 (1 SNP), 4 (2 SNPs), and 10 (1 SNP) were found to be related to ABTS activity. The identified SNPs will be further examined as markers for selecting desirable eggplant varieties and exploring the links between candidate genes, phenolic content, and antioxidant activity. The findings of this study could assist in further study and the development of eggplants with improved health advantages through targeted breeding.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ho-Cheol Ko
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sookyeong Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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42
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Ling X, Liao R, Zhu X. The complete chloroplast genome sequence of Chrysojasminum subhumile and its phylogenetic position within Oleaceae. Mitochondrial DNA B Resour 2023; 8:678-681. [PMID: 37346171 PMCID: PMC10281350 DOI: 10.1080/23802359.2023.2224460] [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: 11/30/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
We assembled and characterized the complete chloroplast genome sequence of Chrysojasminum subhumile (W.W.Sm.) Banfi & Galasso 2014, a valuable horticultural and medicinal plant species. The total genome size was 159,918 bp in length and the GC content was 37.4%. It displayed a circular structure and could be divided into a large single-copy region, a small single-copy region, and a pair of inverted repeat regions. The genome encoded a total of 131 unique genes, including 82 protein-coding genes, 41 tRNA genes, and eight rRNA genes. Among these genes, 17 contained a single intron, and two genes had two introns. Phylogenetic analysis results showed that C. subhumile was closely related to Jasminum.
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Affiliation(s)
- Xinyu Ling
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Rui Liao
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xingfu Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
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Hu K, Sun XQ, Chen M, Lu RS. Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference. FRONTIERS IN PLANT SCIENCE 2023; 14:1196176. [PMID: 37346115 PMCID: PMC10281252 DOI: 10.3389/fpls.2023.1196176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/26/2023] [Indexed: 06/23/2023]
Abstract
Dioscorea sect. Stenophora (Dioscoreaceae) comprises about 30 species that are distributed in the temperate and subtropical regions of the Northern Hemisphere. Despite being evolutionarily "primitive" and medically valuable, genomic resources and molecular studies of this section are still scarce. Here, we conducted low-coverage whole genome sequencing of 11 Stenophora species/subspecies to retrieve their plastome information (whole plastome characteristics, plastome-divergent hotspots, plastome-derived SSRs, etc.) and polymorphic nuclear SSRs, as well as performed comparative plastome and phylogenetic analyses within this section. The plastomes of Stenophora species/subspecies ranged from 153,691 bp (D. zingiberensis) to 154,149 bp (D. biformifolia) in length, and they all contained the same 114 unique genes. All these plastomes were highly conserved in gene structure, gene order and GC content, although variations at the IR/SC borders contributed to the whole length differences among them. The number of plastome-derived SSRs among Stenophora species/subspecies varied from 74 (D. futschauensis) to 93 (D. zingiberensis), with A/T found to be the most frequent one. Seven highly variable regions and 12 polymorphic nuclear SSRs were identified in this section, thereby providing important information for further taxonomical, phylogenetic and population genetic studies. Phylogenomic analyses based on whole plastome sequences and 80 common protein coding genes strongly supported D. biformifolia and D. banzhuana constituted the successive sister species to the remaining sampled species, which could be furtherly divided into three clades. Overall, this study provided a new perspective for plastome evolution of Stenophora, and proved the role of plastome phylogenomic in improving the phylogenetic resolution in this section. These results also provided an important reference for the protection and utilization of this economically important section.
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Affiliation(s)
- Ke Hu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Rui-Sen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
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Zhao SY, Muchuku JK, Liang HY, Wang QF. A complete chloroplast genome of a traditional Chinese medicine herb, Rubia podantha, and phylogenomics of Rubiaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:843-853. [PMID: 37520807 PMCID: PMC10382452 DOI: 10.1007/s12298-023-01302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 08/01/2023]
Abstract
Rubia podantha Diels is endemic to southwestern China and belongs to the family Rubiaceae. It is used in traditional Chinese medicines. To enrich the genetic data and resolve Rubiaceae's phylogeny, we assembled a complete chloroplast (cp) genome of R. podantha using Illumina HiSeq reads. The whole length of the cp genome was 154,866 bp. Annotation using PGA software found 113 genes, including 79 protein coding genes, 30 tRNA genes, and four rRNA genes. The large single-copy region was 84,717 bp, the inverted repeat B (IRa) region was 26,516 bp, the small single copy was 17,117 bp, and the inverted repeats B (IRb) region was 26,516 bp. Moreover, 64 SSRs were identified. Phylogenomic analysis using cp genomes of 109 Rubiaceae species found that R. podantha is closely related to R. cordifola. Rubiaceae was separated into three subfamilies: Ixoroideae, Cinchonoideae, and Rubiodeae. The genus Saprosma was not imbedded within the Spermacoceae alliance as reported in previous studies. Instead, it was imbedded within the Psychotrieae alliance. Divergence time estimation indicated that R. podantha split from its relative R. cordifolia around 1.25 million years ago. The assembled chloroplast genome in this study provided useful molecular information about the evolution of R. podantha and was a basis for phylogenetic analyses of Rubiaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01302-y.
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Affiliation(s)
- Shu-Ying Zhao
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - John K. Muchuku
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200 Kenya
| | - Hai-Ying Liang
- School of Environment and Ecology, Jiangsu Open University, Nanjing, 210036 China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 China
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Cai H, Liu X, Wang W, Ma Z, Li B, Bramley GLC, Zhang D. Phylogenetic relationships and biogeography of Asia Callicarpa (Lamiaceae), with consideration of a long-distance dispersal across the Pacific Ocean -insights into divergence modes of pantropical flora. FRONTIERS IN PLANT SCIENCE 2023; 14:1133157. [PMID: 37255555 PMCID: PMC10225572 DOI: 10.3389/fpls.2023.1133157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/20/2023] [Indexed: 06/01/2023]
Abstract
There are about 140 species of Callicarpa L. 1753 (Lamiaceae), with more species richness in tropical to subtropical Asia and the New World. The genus might provide an insight into the amphi-Pacific disjunction pattern of tropical and subtropical vegetation. This study has greatly improved the phylogenetic underpinning for Callicarpa, derived from more inclusive taxonomic samplings, and employing data on both two-nuclear and eight-chloroplast regions. To address time and patterns of diversification in Callicarpa, we conducted divergence time and biogeographic analyses, and inferred shifts in the distribution areas across the phylogenetic clades. Our phylogenetic results show that Callicarpa is monophyletic with respect to the groups considered, and eight well-supported primary clades were discerned in the combined analyses. Our estimates indicated that the crown group of Callicarpa originates around the Late-Eocene (ca. 36.23 Ma) and diversification within most clades is concentrated in the Miocene and continued to the Pleistocene. In addition, our biogeographic analyses suggested that the probable ancestor of the Callicarpa crown clade originated in East Asia and Southeast Asia. Multiple dispersal and vicariance events contributed to the current distribution of the taxa. Furthermore, this genus expanded eastward out of East and Southeast Asia to the New World by long-distance dispersal, which inspired us to better understand the amphi-Pacific disjunct distribution.
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Affiliation(s)
- Huimin Cai
- Department of Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Xing Liu
- Department of Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Wenqiao Wang
- Department of Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Zhonghui Ma
- Department of Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Nanning, Guangxi, China
| | - Bo Li
- College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | | | - Dianxiang Zhang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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Xiao Y, Li XJ, Jiang XL, Li C, Li XP, Li WP, Tian DK. Spatial genetic patterns and distribution dynamics of Begonia grandis (Begoniaceae), a widespread herbaceous species in China. FRONTIERS IN PLANT SCIENCE 2023; 14:1178245. [PMID: 37235032 PMCID: PMC10206317 DOI: 10.3389/fpls.2023.1178245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Introduction Begonia L., one of the 10 largest plant genera, contains over 2,100 species, most of which have a very limited distribution range. Understanding the spatial genetic structure and distribution dynamics of a widespread species in this genus will contribute to clarifying the mechanism responsible for Begonia speciation. Methods In this study, we used three chloroplast DNA markers (ndhF-rpl32, atpI-atpH, and ndhA intron), coupled with species distribution modeling (SDM), to investigate the population genetic structure and distribution dynamics of Begonia grandis Dryand., the species of Begonia with the widest distribution in China. Results Thirty-five haplotypes from 44 populations clustered into two groups, and haplotype divergence began in the Pleistocene (1.75 Mya). High genetic diversity (H d = 0.894, H T = 0.910), strong genetic differentiation (F ST = 0.835), and significant phylogeographical structure (G ST/N ST = 0.848/0.917, P < 0.05) were observed. The distribution range of B. grandis migrated northwards after the last glacial maximum, but its core distribution area remained stable. Discussion Combined, the observed spatial genetic patterns and SDM results identified the Yunnan-Guizhou Plateau, the Three Gorges region, and the Daba Mountains as potential refugia of B. grandis. BEAST-derived chronogram and haplotype network analysis do not support the Flora Reipublicae Popularis Sinicae and Flora of China for subspecies classification based on morphological characteristics. Our results support the hypothesis that population-level allopatric differentiation may be an important speciation process for the Begonia genus and a key contributor to its rich diversity.
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Affiliation(s)
- Yan Xiao
- College of Life Sciences, Hunan Normal University, Changsha, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xing-Juan Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Chun Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Institute of Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xiang-Peng Li
- Institute of Plant Conservation, Hunan Botanic Garden, Changsha, China
| | - Wei-Ping Li
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Dai-Ke Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Skubic M, Záveská E, Frajman B. Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica. Mol Phylogenet Evol 2023; 185:107805. [PMID: 37127112 DOI: 10.1016/j.ympev.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/03/2023]
Abstract
The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.
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Affiliation(s)
- Maruša Skubic
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria; Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243 Průhonice, Czech Republic
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria.
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Zhou J, He W, Wang J, Liao X, Xiang K, Ma M, Liu Z, Li Y, Tembrock LR, Wu Z, Liu L. The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence. BMC PLANT BIOLOGY 2023; 23:212. [PMID: 37088810 PMCID: PMC10123988 DOI: 10.1186/s12870-023-04218-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is an important food and medicine crop plant, which has been cultivated for 4000 years. A nuclear genome has been generated for this species, while an intraspecific pan-plastome has yet to be produced. As such a detailed understanding of the maternal genealogy of Tartary buckwheat has not been thoroughly investigated. RESULTS In this study, we de novo assembled 513 complete plastomes of Fagopyrum and compared with 8 complete plastomes of Fagopyrum downloaded from the NCBI database to construct a pan-plastome for F. tartaricum and resolve genomic variation. The complete plastomes of the 513 newly assembled Fagopyrum plastome sizes ranged from 159,253 bp to 159,576 bp with total GC contents ranged from 37.76 to 37.97%. These plastomes all maintained the typical quadripartite structure, consisting of a pair of inverted repeat regions (IRA and IRB) separated by a large single copy region (LSC) and a small single copy region (SSC). Although the structure and gene content of the Fagopyrum plastomes are conserved, numerous nucleotide variations were detected from which population structure could be resolved. The nucleotide variants were most abundant in the non-coding regions of the genome and of those the intergenic regions had the most. Mutational hotspots were primarily found in the LSC regions. The complete 521 Fagopyrum plastomes were divided into five genetic clusters, among which 509 Tartary buckwheat plastomes were divided into three genetic clusters (Ft-I/Ft-II/Ft-III). The genetic diversity in the Tartary buckwheat genetic clusters was the greatest in Ft-III, and the genetic distance between Ft-I and Ft-II was the largest. Based on the results of population structure and genetic diversity analysis, Ft-III was further subdivided into three subgroups Ft-IIIa, Ft-IIIb, and Ft-IIIc. Divergence time estimation indicated that the genera Fagopyrum and Rheum (rhubarb) shared a common ancestor about 48 million years ago (mya) and that intraspecies divergence in Tartary buckwheat began around 0.42 mya. CONCLUSIONS The resolution of pan-plastome diversity in Tartary buckwheat provides an important resource for future projects such as marker-assisted breeding and germplasm preservation.
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Affiliation(s)
- Jiawei Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
- College of Science, Health, Engineering and Education, Murdoch University, Western Australia, Perth, 6150, Australia
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Kunli Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingchuan Ma
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Zhang Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zhiqiang Wu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
- College of Horticulture, Shanxi Agricultural University, Shanxi, 030801, China.
| | - Longlong Liu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, China.
- Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan, 030031, China.
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Yoichi W, Tamaki I, Oh SH, Nagano AJ, Uehara K, Tomaru N, Abe H. The evolutionary history of rice azaleas (Rhododendron tschonoskii alliance) involved niche evolution to a montane environment. AMERICAN JOURNAL OF BOTANY 2023; 110:e16166. [PMID: 37074769 DOI: 10.1002/ajb2.16166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 05/03/2023]
Abstract
PREMISE The formation of isolated montane geography on islands promotes evolution, speciation, and then radiation if there are ecological changes. Thus, investigating evolutionary histories of montane species and associated ecological changes may help efforts to understand how endemism formed in islands' montane floras. To explore this process, we investigated the evolutionary history of the Rhododendron tschonoskii alliance, which grows in montane environments of the Japanese archipelago and the Korean Peninsula. METHODS We studied the five species in the R. tschonoskii alliance and 30 outgroup species, using genome-wide single-nucleotide polymorphisms and cpDNA sequences, in association with environmental analyses. RESULTS The monophyletic R. tschonoskii alliance diverged since the late Miocene. Species in the alliance currently inhabit a cold climatic niche that is largely different from that of the outgroup species. We observed clear genetic and niche differentiations between the taxa of the alliance. CONCLUSIONS The association of the alliance's evolution with the formation of cooler climates on mountains indicates that it was driven by global cooling since the mid-Miocene and by rapid uplift of mountains since the Pliocene. The combination of geographic and climatic isolation promoted high genetic differentiation between taxa, which has been maintained by climatic oscillations since the Quaternary.
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Affiliation(s)
- Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Ichiro Tamaki
- Gifu Academy of Forest Science and Culture, 88 Sodai, Mino, Gifu, Japan
| | - Sang-Hun Oh
- Department of Biology, Daejeon University, 62 Daehak-ro, Dong-gu, Daejeon, 34520, South Korea
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Koichi Uehara
- College of Liberal Arts and Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Japan
| | - Harue Abe
- Sado Island Center for Ecological Sustainability, Niigata University, 94-2 Koda, Sado, Niigata, 952-2206, Japan
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Marinho RC, Mendes-Rodrigues C, Resende-Moreira LC, Lovato MB, Bonetti AM, Oliveira PE. Phylogeography of Eriotheca species complex: insights into the origin and range expansion of apomictic and polyploid trees in Neotropical Savannas. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:457-467. [PMID: 36728131 DOI: 10.1111/plb.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Polyploidy and whole genome duplication are major evolutionary drivers in plants. Climate variations during the Pleistocene have influenced distribution and range expansion worldwide. Similar trends have been reported for Cerrado plants, but no attempt has been made to link phylogeography with ploidy and breeding changes. Thus, we aimed to (i) assess ploidy and genome size of Eriotheca estevesiae Carv.-Sobr., and compare it with E. pubescens (Mart.) Schott & Endl. (Both included into the Eriotheca Stellate Trichome Species Complex - ESTSC). (ii) Subsequently, we investigated their phylogeography to see whether genetic structure and range expansion trends were similar to those previously described for the Cerrado biome. Finally (iii), we discuss whether ESTSC phylogeographic patterns could be associated with geographic parthenogenesis processes. Common cytogenetic techniques and flow cytometry were used to confirm chromosome number and genome size of E. estevesiae. We used three cpDNA regions to analyse 14 ESTSC Cerrado populations, for which we also obtained ploidy level and breeding information. We investigated haplotype diversity, population structure and tested neutrality, aiming to reconstruct phylogeographic scenarios. We found three ploidy levels and eight cpDNA haplotypes in ESTSC, one shared by most populations. Haplotype and ploidy distribution corroborated that E. pubescens, the widely distributed polyploid and apomictic species, may have originated from northern diploid and probably sexual E. estevesiae. Matrilinear cpDNA links support the idea that apomixis and polyploidy in ESTSC may have allowed range expansion during the Pleistocene, in a process analogous to the geographic parthenogenesis described elsewhere.
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Affiliation(s)
- R C Marinho
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - C Mendes-Rodrigues
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
- Faculdade de Medicina, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - L C Resende-Moreira
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M B Lovato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A M Bonetti
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - P E Oliveira
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
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