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Kelsang GA, Ni L, Zhao Z. Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim. DNA Res 2024; 31:dsae022. [PMID: 39017645 PMCID: PMC11375616 DOI: 10.1093/dnares/dsae022] [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: 11/01/2023] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/18/2024] Open
Abstract
Gentiana straminea Maxim. is a perennial herb and mainly distributed in the Qinghai-Tibetan Plateau. To adapt to the extreme environment, it has developed particular morphological, physiological, and genetic structures. Also, rich in iridoids, it is one of the original plants of traditional Chinese herb 'Qinjiao'. Herein, we present its first chromosome-level genome sequence assembly and compare it with the genomes of other Gentiana species to facilitate the analysis of genomic characteristics. The assembled genome size of G. straminea was 1.25 Gb, with a contig N50 of 7.5 Mb. A total of 96.08% of the genome sequences was anchored on 13 pseudochromosomes, with a scaffold N50 of 92.70 Mb. A total of 54,310 protein-coding genes were predicted, 80.25% of which were functionally annotated. Comparative genomic analyses indicated that G. straminea experienced two whole-genome duplication events after the γ whole-genome triplication with other eudicots, and it diverged from other Gentiana species at ~3.2 Mya. A total of 142 enzyme-coding genes related to iridoid biosynthesis were identified in its genome. Additionally, we identified differences in the number and expression patterns of iridoid biosynthetic pathway genes in G. straminea compared with two other Gentiana species by integrating whole-genome sequence and transcriptomic analyses.
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Affiliation(s)
- Gyab Ala Kelsang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Mentseekhang, Traditional Tibetan Hospital, Lhasa 850000, China
| | - Lianghong Ni
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhili Zhao
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Dalla Costa TP, Silva MC, de Santana Lopes A, Pacheco TG, da Silva GM, de Oliveira JD, de Baura VA, Balsanelli E, de Souza EM, de Oliveira Pedrosa F, Rogalski M. The plastomes of Lepismium cruciforme (Vell.) Miq and Schlumbergera truncata (Haw.) Moran reveal tribe-specific rearrangements and the first loss of the trnT-GGU gene in Cactaceae. Mol Biol Rep 2024; 51:957. [PMID: 39230768 DOI: 10.1007/s11033-024-09871-1] [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: 05/23/2024] [Accepted: 08/19/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND Recent studies have revealed atypical features in the plastomes of the family Cactaceae, the largest lineage of succulent species adapted to arid and semi-arid regions. Most plastomes sequenced to date are from short-globose and cylindrical cacti, while little is known about plastomes of epiphytic cacti. Published cactus plastomes reveal reduction and complete loss of IRs, loss of genes, pseudogenization, and even degeneration of tRNA structures. Aiming to contribute with new insights into the plastid evolution of Cactaceae, particularly within the tribe Rhipsalideae, we de novo assembled and analyzed the plastomes of Lepismium cruciforme and Schlumbergera truncata, two South American epiphytic cacti. METHODS AND RESULTS Our data reveal many gene losses in both plastomes and the first loss of functionality of the trnT-GGU gene in Cactaceae. The trnT-GGU is a pseudogene in L. cruciforme plastome and appears to be degenerating in the tribe Rhipsalideae. Although the plastome structure is conserved among the species of the tribe Rhipsalideae, with tribe-specific rearrangements, we mapped around 200 simple sequence repeats and identified nine nucleotide polymorphism hotspots, useful to improve the phylogenetic resolutions of the Rhipsalideae. Furthermore, our analysis indicated high gene divergence and rapid evolution of RNA editing sites in plastid protein-coding genes in Cactaceae. CONCLUSIONS Our findings show that some characteristics of the Rhipsalideae tribe are conserved, such as plastome structure with IRs containing only the ycf2 and two tRNA genes, structural degeneration of the trnT-GGU gene and ndh complex, and lastly, pseudogenization of rpl33 and rpl23 genes, both plastid translation-related genes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brasil.
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Sun S, Pan Z, Fu Y, Wang S, Fu P. Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae. Ecol Evol 2024; 14:e70239. [PMID: 39224159 PMCID: PMC11368500 DOI: 10.1002/ece3.70239] [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: 03/28/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.
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Affiliation(s)
- Shan‐Shan Sun
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Zhi‐Yong Pan
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Yu Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Shen‐Jue Wang
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
| | - Peng‐Cheng Fu
- School of Life ScienceLuoyang Normal UniversityLuoyangChina
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Park S, An B, Park S. Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae). BMC PLANT BIOLOGY 2024; 24:303. [PMID: 38644497 PMCID: PMC11034061 DOI: 10.1186/s12870-024-05025-4] [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: 07/12/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Corydalis DC., the largest genus in the family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of Corydalis show evolutionary changes, including syntenic arrangements, gene losses and duplications, and IR boundary shifts. However, little is known about the evolution of the mitochondrial genome (mitogenome) in Corydalis. Both the organelle genomes and transcriptomes are needed to better understand the relationships between the patterns of evolution in mitochondrial and plastid genomes. RESULTS We obtained complete plastid and mitochondrial genomes from Corydalis pauciovulata using a hybrid assembly of Illumina and Oxford Nanopore Technologies reads to assess the evolutionary parallels between the organelle genomes. The mitogenome and plastome of C. pauciovulata had sizes of 675,483 bp and 185,814 bp, respectively. Three ancestral gene clusters were missing from the mitogenome, and expanded IR (46,060 bp) and miniaturized SSC (202 bp) regions were identified in the plastome. The mitogenome and plastome of C. pauciovulata contained 41 and 67 protein-coding genes, respectively; the loss of genes was a plastid-specific event. We also generated a draft genome and transcriptome for C. pauciovulata. A combination of genomic and transcriptomic data supported the functional replacement of acetyl-CoA carboxylase subunit β (accD) by intracellular transfer to the nucleus in C. pauciovulata. In contrast, our analyses suggested a concurrent loss of the NADH-plastoquinone oxidoreductase (ndh) complex in both the nuclear and plastid genomes. Finally, we performed genomic and transcriptomic analyses to characterize DNA replication, recombination, and repair (DNA-RRR) genes in C. pauciovulata as well as the transcriptomes of Liriodendron tulipifera and Nelumbo nuicifera. We obtained 25 DNA-RRR genes and identified their structure in C. pauciovulata. Pairwise comparisons of nonsynonymous (dN) and synonymous (dS) substitution rates revealed that several DNA-RRR genes in C. pauciovulata have higher dN and dS values than those in N. nuicifera. CONCLUSIONS The C. pauciovulata genomic data generated here provide a valuable resource for understanding the evolution of Corydalis organelle genomes. The first mitogenome of Papaveraceae provides an example that can be explored by other researchers sequencing the mitogenomes of related plants. Our results also provide fundamental information about DNA-RRR genes in Corydalis and their related rate variation, which elucidates the relationships between DNA-RRR genes and organelle genome stability.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
| | - Boram An
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, South Korea.
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Fu PC, Guo QQ, Chang D, Gao QB, Sun SS. Cryptic diversity and rampant hybridization in annual gentians on the Qinghai-Tibet Plateau revealed by population genomic analysis. PLANT DIVERSITY 2024; 46:194-205. [PMID: 38807911 PMCID: PMC11128845 DOI: 10.1016/j.pld.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 05/30/2024]
Abstract
Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of FST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qiao-Qiao Guo
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Di Chang
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
| | - Qing-Bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, PR China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang 471934, PR China
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Tu XD, Lin WJ, Fu HH, Lin YZ, Shen J, Chen S, Liu ZJ, Li MH, Chen SP. Comparative Analysis of Six Complete Plastomes of Tripterospermum spp. Int J Mol Sci 2024; 25:2534. [PMID: 38473781 DOI: 10.3390/ijms25052534] [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: 12/13/2023] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
The Tripterospermum, comprising 34 species, is a genus of Gentianaceae. Members of Tripterospermum are mostly perennial, entwined herbs with high medicinal value and rich in iridoids, xanthones, flavonoids, and triterpenes. However, our inadequate understanding of the differences in the plastid genome sequences of Tripterospermum species has severely hindered the study of their evolution and phylogeny. Therefore, we first analyzed the 86 Gentianae plastid genomes to explore the phylogenetic relationships within the Gentianae subfamily where Tripterospermum is located. Then, we analyzed six plastid genomes of Tripterospermum, including two newly sequenced plastid genomes and four previously published plastid genomes, to explore the plastid genomes' evolution and phylogenetic relationships in the genus Tripterospermum. The Tripterospermum plastomes have a quadripartite structure and are between 150,929 and 151,350 bp in size. The plastomes of Tripterospermum encoding 134 genes were detected, including 86 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and three pseudogenes (infA, rps19, and ycf1). The result of the comparison shows that the Tripterospermum plastomes are very conserved, with the total plastome GC content ranging from 37.70% to 37.79%. In repeat sequence analysis, the number of single nucleotide repeats (A/T) varies among the six Tripterospermum species, and the identified main long repeat types are forward and palindromic repeats. The degree of conservation is higher at the SC/IR boundary. The regions with the highest divergence in the CDS and the intergenic region (IGS) are psaI and rrn4.5-rrn5, respectively. The average pi of the CDS and the IGS are only 0.071% and 0.232%, respectively, indicating that the Tripterospermum plastomes are highly conserved. Phylogenetic analysis indicated that Gentianinae is divided into two clades, with Tripterospermum as a sister to Sinogeniana. Phylogenetic trees based on CDS and CDS + IGS combined matrices have strong support in Tripterospermum. These findings contribute to the elucidation of the plastid genome evolution of Tripterospermum and provide a foundation for further exploration and resource utilization within this genus.
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Affiliation(s)
- Xiong-De Tu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wen-Jun Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hou-Hua Fu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi-Zhe Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jun Shen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuai Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ming-He Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Pin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Fu PC, Twyford AD, Hao YT, Zhang Y, Chen SL, Sun SS. Hybridization and divergent climatic preferences drive divergence of two allopatric Gentiana species on the Qinghai-Tibet Plateau. ANNALS OF BOTANY 2023; 132:1271-1288. [PMID: 37963010 PMCID: PMC10902892 DOI: 10.1093/aob/mcad179] [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: 06/21/2023] [Revised: 10/19/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND AND AIMS Exploring how species diverge is vital for understanding the drivers of speciation. Factors such as geographical separation and ecological selection, hybridization, polyploidization and shifts in mating system are all major mechanisms of plant speciation, but their contributions to divergence are rarely well understood. Here we test these mechanisms in two plant species, Gentiana lhassica and G. hoae, with the goal of understanding recent allopatric species divergence on the Qinghai-Tibet Plateau (QTP). METHODS We performed Bayesian clustering, phylogenetic analysis and estimates of hybridization using 561 302 nuclear genomic single nucleotide polymorphisms (SNPs). We performed redundancy analysis, and identified and annotated species-specific SNPs (ssSNPs) to explore the association between climatic preference and genetic divergence. We also estimated genome sizes using flow cytometry to test for overlooked polyploidy. KEY RESULTS Genomic evidence confirms that G. lhassica and G. hoae are closely related but distinct species, while genome size estimates show divergence occurred without polyploidy. Gentiana hoae has significantly higher average FIS values than G. lhassica. Population clustering based on genomic SNPs shows no signature of recent hybridization, but each species is characterized by a distinct history of hybridization with congeners that has shaped genome-wide variation. Gentiana lhassica has captured the chloroplast and experienced introgression with a divergent gentian species, while G. hoae has experienced recurrent hybridization with related taxa. Species distribution modelling suggested range overlap in the Last Interglacial Period, while redundancy analysis showed that precipitation and temperature are the major climatic differences explaining the separation of the species. The species differ by 2993 ssSNPs, with genome annotation showing missense variants in genes involved in stress resistance. CONCLUSIONS This study suggests that the distinctiveness of these species on the QTP is driven by a combination of hybridization, geographical isolation, mating system differences and evolution of divergent climatic preferences.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Alex D Twyford
- Institute of Ecology and Evolution, The University of Edinburgh, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Yu-Tong Hao
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Yue Zhang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 810001 Xining, P. R. China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, Luoyang 471934, P. R. China
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Hou Y, Zhang Y, Yu J, Wang X. Characteristics of the complete chloroplast genome of Swertia divaricata Harry Sm. (Gentianaceae) and its phylogenetic inference. Mitochondrial DNA B Resour 2023; 8:1132-1136. [PMID: 37928401 PMCID: PMC10621253 DOI: 10.1080/23802359.2023.2270211] [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: 04/09/2023] [Accepted: 10/07/2023] [Indexed: 11/07/2023] Open
Abstract
Swertia divaricata Harry Sm., 1965, (Gentianaceae) is a perennial herb endemic to Northwest Yunnan, China, belonging to the species-rich genus Swertia. It possesses unique morphological features but its systematic position remains uncertain. To determine its phylogenetic placement, the complete plastid genome of S. divaricata was assembled utilizing high-throughput sequencing data. The genome is circular, spanning 152,073 bp, and comprises a large single-copy (LSC) region of 82,470 bp, a small single-copy (SSC) region of 18,153 bp, and two inverted repeats (IR) regions, each 25,725 bp. A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The plastome of S. divaricata exhibits a structure and gene composition highly similar to those of other Swertia plastomes. Phylogenetic analysis indicated that S. divaricata is closely related to S. erythrosticta, sister to a subclade comprising species from sections Swertia and Apterae. The plastome sequence described herein constitutes a valuable contribution to phylogenetic and evolutionary research on Swertia.
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Affiliation(s)
- Yingying Hou
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Yulong Zhang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Integrated Traditional Chinese and Western Medicine, The Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Jing Yu
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjie Wang
- Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Li ZZ, Lehtonen S, Chen JM. The dynamic history of plastome structure across aquatic subclass Alismatidae. BMC PLANT BIOLOGY 2023; 23:125. [PMID: 36869282 PMCID: PMC9985265 DOI: 10.1186/s12870-023-04125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The rapidly increasing availability of complete plastomes has revealed more structural complexity in this genome under different taxonomic levels than expected, and this complexity provides important evidence for understanding the evolutionary history of angiosperms. To explore the dynamic history of plastome structure across the subclass Alismatidae, we sampled and compared 38 complete plastomes, including 17 newly assembled, representing all 12 recognized families of Alismatidae. RESULT We found that plastomes size, structure, repeat elements, and gene content were highly variable across the studied species. Phylogenomic relationships among families were reconstructed and six main patterns of variation in plastome structure were revealed. Among these, the inversion from rbcL to trnV-UAC (Type I) characterized a monophyletic lineage of six families, but independently occurred also in Caldesia grandis. Three independent ndh gene loss events were uncovered across the Alismatidae. In addition, we detected a positive correlation between the number of repeat elements and the size of plastomes and IR in Alismatidae. CONCLUSION In our study, ndh complex loss and repeat elements likely contributed to the size of plastomes in Alismatidae. Also, the ndh loss was more likely related to IR boundary changes than the adaptation of aquatic habits. Based on existing divergence time estimation, the Type I inversion may have occurred during the Cretaceous-Paleogene in response to the extreme paleoclimate changes. Overall, our findings will not only allow exploring the evolutionary history of Alismatidae plastome, but also provide an opportunity to test if similar environmental adaptations result in convergent restructuring in plastomes.
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Affiliation(s)
- Zhi-Zhong Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, Turku, 20014, Finland.
| | - Jin-Ming Chen
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Comparative transcriptome analyses of three Gentiana species provides signals for the molecular footprints of selection effects and the phylogenetic relationships. Mol Genet Genomics 2023; 298:399-411. [PMID: 36592219 DOI: 10.1007/s00438-022-01991-2] [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: 11/08/2021] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
Species in Gentiana section Cruciata are important alpine plants with a center of diversity and speciation in Qinghai-Tibet Plateau (QTP), and some of these species are sympatrically distributed in northeastern QTP. Studies on genome features and natural selection signatures of sympatric species in section Crucata have been impeded by a lack of genomic resources. Here, we showed transcript characterizations and molecular footprints of selection effects on G. straminea, G. dahurica and G. officinalis based on the comparative transcriptome. A total of 62.97 Gb clean reads were obtained with unigene numbers per species ranging from 141,819 to 236,408 after assembly. We found that these three species had similar distribution of functional categories in different databases, and key enzyme-encoding genes involved in the iridoids biosynthesis were also obtained. The selective pressure analyses indicated that most paired orthologs between these three species were subject to negative selection, and only a low proportion of the orthologs that underwent positive selection were detected. We found that some positive selected genes were involved in "catalytic activity", "metabolic process", "response to stimulus" and "response to stress". Besides, large numbers of SSR primer pairs with transferabilities were successfully designed based on the available transcriptome datasets of three Gentiana species. The phylogenetic relationships reconstructed based on 352 single-copy nuclear genes provided a rough phylogenetic framework for this genus and confirmed the monophyly of section Cruciata. Our study not only provides insights for the natural selection effects on sympatric Gentiana species, but also enhances future genetic breeding or evolutionary studies on Qinjiao species.
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Comparison of Boraginales Plastomes: Insights into Codon Usage Bias, Adaptive Evolution, and Phylogenetic Relationships. DIVERSITY 2022. [DOI: 10.3390/d14121104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Boraginales (Boraginaceae a.l.) comprise more than 2450 species worldwide. However, little knowledge exists of the characteristics of the complete plastid genome. In this study, three new sequences representing the first pt genome of Heliotropiaceae and Cordiaceae were assembled and compared with other Boraginales species. The pt genome sizes of Cordia dichotoma, Heliotropium arborescens, and Tournefortia montana were 151,990 bp, 156,243 bp, and 155,891 bp, respectively. Multiple optimal codons were identified, which may provide meaningful information for enhancing the gene expression of Boraginales species. Furthermore, codon usage bias analyses revealed that natural selection and other factors may dominate codon usage patterns in the Boraginales species. The boundaries of the IR/LSC and IR/SSC regions were significantly different, and we also found a signal of obvious IR region expansion in the pt genome of Nonea vesicaria and Arnebia euchroma. Genes with high nucleic acid diversity (pi) values were also calculated, which may be used as potential DNA barcodes to investigate the phylogenetic relationships in Boraginales. psaI, rpl33, rpl36, and rps19 were found to be under positive selection, and these genes play an important role in our understanding of the adaptive evolution of the Boraginales species. Phylogenetic analyses implied that Boraginales can be divided into two groups. The existence of two subfamilies (Lithospermeae and Boragineae) in Boraginaceae is also strongly supported. Our study provides valuable information on pt genome evolution and phylogenetic relationships in the Boraginales species.
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12
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Yu J, Fu P, Sun S. Complete plastid genome of Gentiana zollingeri Fawcett (Gentianaceae) and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:2063-2066. [PMCID: PMC9744209 DOI: 10.1080/23802359.2022.2152644] [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] [Indexed: 12/14/2022] Open
Abstract
Gentiana zollingeri Fawcett (Gentianaceae) belongs to the most species-rich section, Chondrophyllae, in the Gentianaceae, but its phylogenetic relationship with other members of this section is unclear. To confirm its phylogenetic position, the complete plastid genome of G. zollingeri was determined and analyzed. The plastome was sequenced using the Illumina HiSeq platform, assembled with GetOrganelle, and annotated with GeSeq. The genome is circular with a length of 130,762 bp. It contains a large single-copy (LSC) region of 74,236 bp, a small single-copy (SSC) region of 10,598 bp, and two inverted repeat (IR) regions of 22,964 bp each. The plastome of G. zollingeri shows considerable structural differences from those of other Gentiana plastomes, such as the absence of the ndh gene. In phylogenetic analyses, section Chondrophyllae, including G. zollingeri and its sisters, formed a long branch sistering with section Cruciata. The plastome sequence described here represents an important contribution to phylogenetic and evolutionary studies on Gentiana.
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Affiliation(s)
- Jing Yu
- Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pengcheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Shanshan Sun
- School of Life Science, Luoyang Normal University, Luoyang, China,CONTACT Shanshan Sun School of Life Science, Luoyang Normal University, Luoyang, China
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Fu P, Favre A, Wang R, Huang Y, Sun S. Between allopatry and secondary contact: differentiation and hybridization among three sympatric Gentiana species in the Qinghai-Tibet Plateau. BMC PLANT BIOLOGY 2022; 22:504. [PMID: 36307765 PMCID: PMC9615307 DOI: 10.1186/s12870-022-03879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mountains of the world host a significant portion of all terrestrial biodiversity, and the region of the Qinghai-Tibet Plateau (QTP) stands as one of the most remarkable mountain regions on Earth. Because many explosive radiations occurred there, the QTP is a natural laboratory which is ideal to investigate patterns and processes linked to speciation and diversification. Indeed, understanding how closely related and sympatric species diverged is vital to explore drivers fostering speciation, a topic only rarely investigated in the QTP. By combining genomic and environmental data, we explored the speciation process among three closely related and sympatric species, Gentiana hexaphylla, G. lawrencei and G. veitchiorum in the QTP region. RESULTS Combining genome sizes and cytological data, our results showed that G. hexaphylla and G. veitchiorum are diploid, whereas G. lawrencei is tetraploid. Genetic clustering and phylogenetic reconstruction based on genomic SNPs indicated a clear divergence among the three species. Bayesian clustering, migrant, and D-statistic analyses all showed an obvious signature of hybridization among the three species, in particular between G. lawrencei and both G. hexaphylla and G. veitchiorum in almost all populations. Environmental variables related to precipitation and particularly temperature showed significant differences among the three gentians, and in fact a redundancy analysis confirmed that temperature and precipitation were the major climatic factors explaining the genetic differentiation among the three species. CONCLUSION Our study suggested that ancient hybridization, polyploidization, geological isolation and the evolution of different climatic preferences were all likely to be involved in the divergence of the three Gentiana species, as may be the case for many other taxa in the QTP region.
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Affiliation(s)
- Pengcheng Fu
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Adrien Favre
- Regional nature park of the Trient Valley, La Place 24, 1922, Salvan, Switzerland
| | - Rui Wang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Yizhuo Huang
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China
| | - Shanshan Sun
- School of Life Science, Luoyang Normal University, 6 Jiqing Road, 471934, Luoyang, P. R. China.
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Chu R, Xu X, Lu Z, Ma Y, Cheng H, Zhu S, Bakker FT, Schranz ME, Wei Z. Plastome-based phylogeny and biogeography of Lactuca L. (Asteraceae) support revised lettuce gene pool categories. FRONTIERS IN PLANT SCIENCE 2022; 13:978417. [PMID: 36311071 PMCID: PMC9597326 DOI: 10.3389/fpls.2022.978417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major Lactuca lineages. The results showed that Lactuca species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce (Lactuca sativa L.) and its gene pool relatives were found to have one unique pseudogene (ψ ndhF), and accD, atpF, cemA, clpP, and rpl22 showed signs of positive selection. Our phylogenomic analysis demonstrated that Lactuca is monophyletic after excluding Lactuca alatipes Collett and Hemsl and AE Lactuca species. AE Lactuca species are morphologically distinct from core Lactuca lineage and need to be excluded from Lactua. The core Lactuca species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of Lactuca, revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.
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Affiliation(s)
- Ran Chu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuemin Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenwei Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yonggui Ma
- School of Life Sciences, Qinghai Normal University, Xining, China
- Key Laboratory of Medicinal Animal and Plant Resources of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shixin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Freek T. Bakker
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Zhou T, Bai G, Hu Y, Ruhsam M, Yang Y, Zhao Y. De novo genome assembly of the medicinal plant Gentiana macrophylla provides insights into the genomic evolution and biosynthesis of iridoids. DNA Res 2022; 29:6748869. [PMID: 36197098 PMCID: PMC9724787 DOI: 10.1093/dnares/dsac034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Gentiana macrophylla is a perennial herb in the Gentianaceae family, whose dried roots are used in traditional Chinese medicine. Here, we assembled a chromosome-level genome of G. macrophylla using a combination of Nanopore, Illumina, and Hi-C scaffolding approaches. The final genome size was ~1.79 Gb (contig N50 = 720.804 kb), and 98.89% of the genome sequences were anchored on 13 pseudochromosomes (scaffold N50 = 122.73 Mb). The genome contained 55,337 protein-coding genes, and 73.47% of the assemblies were repetitive sequences. Genome evolution analysis indicated that G. macrophylla underwent two rounds of whole-genome duplication after the core eudicot γ genome triplication event. We further identified candidate genes related to the biosynthesis of iridoids, and the corresponding gene families mostly expanded in G. macrophylla. In addition, we found that root-specific genes are enriched in pathways involved in defense responses, which may greatly improve the biological adaptability of G. macrophylla. Phylogenomic analyses showed a sister relationship of asterids and rosids, and all Gentianales species formed a monophyletic group. Our study contributes to the understanding of genome evolution and active component biosynthesis in G. macrophylla and provides important genomic resource for the genetic improvement and breeding of G. macrophylla.
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Affiliation(s)
- Tao Zhou
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
| | | | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Yanci Yang
- School of Biological Science and Technology, Baotou Teachers’ College, Baotou, China
| | - Yuemei Zhao
- Corresponding author: Tel. +86 29 8265 5424. (T.Z.); (Y.Z.)
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Fu PC, Sun SS, Hollingsworth PM, Chen SL, Favre A, Twyford AD. Population genomics reveal deep divergence and strong geographical structure in gentians in the Hengduan Mountains. FRONTIERS IN PLANT SCIENCE 2022; 13:936761. [PMID: 36092450 PMCID: PMC9453878 DOI: 10.3389/fpls.2022.936761] [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: 05/05/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise F ST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, China
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, China
| | | | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History Museum, Frankfurt, Germany
| | - Alex D. Twyford
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
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17
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Fu P, Chen S, Sun S, Favre A. Strong plastid degradation is consistent within section Chondrophyllae, the most speciose lineage of Gentiana. Ecol Evol 2022; 12:e9205. [PMID: 35991284 PMCID: PMC9379351 DOI: 10.1002/ece3.9205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
Recovering phylogenetic relationships in lineages experiencing intense diversification has always been a persistent challenge in evolutionary studies, including in Gentiana section Chondrophyllae sensu lato (s.l.). Indeed, this subcosmopolitan taxon encompasses more than 180 mostly annual species distributed around the world. We sequenced and assembled 22 new plastomes representing 21 species in section Chondrophyllae s.l. In addition to previously released plastome data, our study includes all main lineages within the section. We reconstructed their phylogenetic relationships based on protein-coding genes and recombinant DNA (rDNA) cistron sequences, and then investigated plastome structural evolution as well as divergence time. Despite an admittedly humble species cover overall, we recovered a well-supported phylogenetic tree based on plastome data, and found significant discordance between phylogenetic relationships and taxonomic treatments. Our results show that G. capitata and G. leucomelaena diverged early within the section, which is then further divided into two clades. The divergence time estimation showed that section Chondrophyllae s.l. evolved in the second half of the Oligocene. We found that section Chondrophyllae s.l. had the smallest average plastome size (128 KB) in tribe Gentianeae (Gentianaceae), with frequent gene and sequence losses such as the ndh complex and its flanking regions. In addition, we detected both expansion and contraction of the inverted repeat (IR) regions. Our study suggests that plastome degradation parallels the diversification of this group, and illustrates the strong discordance between phylogenetic relationships and taxonomic treatments, which now need to be carefully revised.
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Affiliation(s)
- Peng‐Cheng Fu
- School of Life Science, Luoyang Normal UniversityLuoyangP. R. China
| | - Shi‐Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningP. R. China
| | - Shan‐Shan Sun
- School of Life Science, Luoyang Normal UniversityLuoyangP. R. China
| | - Adrien Favre
- Senckenberg Research Institute and Natural History MuseumFrankfurt am MainGermany
- Regional Nature Park of the Trient ValleySalvanSwitzerland
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Qu XJ, Zhang XJ, Cao DL, Guo XX, Mower JP, Fan SJ. Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes. Mol Phylogenet Evol 2022; 174:107544. [PMID: 35690375 DOI: 10.1016/j.ympev.2022.107544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/19/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species. Most Persicarieae plastomes exhibit a conserved structure and content relative to other flowering plants. However, Koenigia delicatula has lost functional copies of all ndh genes and the intron from atpF. In addition, the rpl32 gene was relocated in the K. delicatula plastome, which likely occurred via overlapping inversions or differential expansion and contraction of the inverted repeat. The highly supported but conflicting relationships between plastome and mitochondrial trees and among gene trees complicates the circumscription of Koenigia, which could be caused by rapid diversification within a short period. Moreover, the plastome and mitochondrial trees revealed correlated variation in substitution rates among Persicarieae species, suggesting a shared underlying mechanism promoting evolutionary rate variation in both organellar genomes. The divergence of dwarf K. delicatula from other Koenigia species may be associated with the well-known Eocene Thermal Maximum 2 or Early Eocene Climatic Optimum event, while diversification of the core-Koenigia clade associates with the Mid-Miocene Climatic Optimum and the uplift of Qinghai-Tibetan Plateau and adjacent areas.
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Affiliation(s)
- Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China
| | - Dong-Ling Cao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China
| | - Xiu-Xiu Guo
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA.
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan 250014, Shandong, China.
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Feng Z, Zheng Y, Jiang Y, Miao YJ, Luo GM, Huang L. Complete chloroplast genome of Gentianopsis barbata and comparative analysis with related species from Gentianaceae. Genome 2022; 65:363-375. [DOI: 10.1139/gen-2021-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gentianopsis barbata is an essential medicinal plant in China with high ornamental and medicinal values. Unfortunately, the study of the chloroplast genome of this plant still has a gap. This study sequenced and characterized the complete chloroplast genome of G. barbata. The complete chloroplast genome of G. barbata is a typical circular structure with 151,123 bp. It consists of a large single-copy region (82,690 bp) and a small single-copy region (17,887 bp) separated by a pair of inverted repeats (25,273 bp), which covers 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Repeat analysis showed the highest frequency of palindrome. Thirty-seven simple sequence repeats were identified, most of which were single nucleotides. The bayesian inference tree, maximum likelihood tree, and neighbor joining tree suggested that G. barbata is grouped with Gentianopsis grandis and Gentianopsis paludosa. The divergence time analysis showed that G. barbata diverged at 1.243 Mya. Comparative chloroplast analysis can reveal interspecific diversity, and regions with high variation can be used to develop molecular markers applicable to various research areas. Our results provide new insight into plastome evolution and valuable resource for further studies on G. barbata.
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Affiliation(s)
- Zhan Feng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yan Zheng
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, Jiangxi, China
| | - Yuan Jiang
- Chinese Academy of Medical Sciences & Peking Union Medical College, 12501, Beijing, China
- Dali University, 66359, Dali, China
| | - Yu Jing Miao
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, Beijing, China
| | - Guang Ming Luo
- Jiangxi University of Traditional Chinese Medicine, 74582, Nanchang, China
| | - Linfang Huang
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medicinal Plant Development, 198148, Haidian District, China
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Dalla Costa TP, Silva MC, de Santana Lopes A, Gomes Pacheco T, de Oliveira JD, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes. PLANTA 2022; 255:57. [PMID: 35113261 DOI: 10.1007/s00425-022-03841-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Ya HY, Miao YW. Complete plastid genome of Gentiana leucomelaena Maxim. (Gentianaceae) and phylogenetic analysis. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2953-2954. [PMID: 34553055 PMCID: PMC8451681 DOI: 10.1080/23802359.2021.1972872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The complete plastid genome of Gentiana leucomelaena Maxim., belonging to the most species-rich section Chondrophyllae in Gentiana, was determined and analyzed in this study. It has a circular-mapping molecular with the length of 131,856 bp, the shortest one among all available Gentiana plastomes. Gentiana leucomelaena has gene mutation, for example ndh and rpl2 intron, and reversed SSC region comparing with the available species in sections Cruciata, Frigida, Kudoa, Isomeria and Microsperma. Phylogenetic analysis showed that G. leucomelaena clustered together with section Cruciata with a long branch. The plastome provides in this work will contribute to elucidate the phylogenetics and evolution in Gentiana.
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Affiliation(s)
- Hui-Yuan Ya
- School of Food and Drug, Luoyang Normal University, Luoyang, People's Republic of China
| | - Yu-Wei Miao
- Construction Management Committee of Xining Garden Expo Park and XiBu Forest Park, Xining, People's Republic of China
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