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Kwok van der Giezen FM, Viljoen A, Campbell-Clause L, Dao NT, Colas des Francs-Small C, Small I. Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:445-459. [PMID: 38652016 DOI: 10.1111/tpj.16775] [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: 02/01/2024] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.
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Affiliation(s)
- Farley M Kwok van der Giezen
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Amy Viljoen
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Leni Campbell-Clause
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Nhan Trong Dao
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Catherine Colas des Francs-Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
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Javaid N, Ramzan M, Jabeen S, Du Y, Anwar M, Xiqiang S. The chloroplast genome of Chrozophora sabulosa Kar. & Kir. and its exploration in the evolutionary position uncertainty of genus Chrozophora. BMC Genomics 2024; 25:597. [PMID: 38877411 PMCID: PMC11177538 DOI: 10.1186/s12864-024-10366-3] [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: 06/02/2023] [Accepted: 04/29/2024] [Indexed: 06/16/2024] Open
Abstract
Chrozophora sabulosa Kar. & Kir. is a biennial herbaceous plant that belongs to the Euphorbiaceae family and has medicinal properties. This research aimed to identify the genetic characteristics and phylogenetic position of the Chrozophora genus within the Euphorbiaceae family. The evolutionary position of the Chrozophora genus was previously unknown due to insufficient research. Therefore, to determine the evolutionary link between C. sabulosa and other related species, we conducted a study using the NGS Illumina platform to sequence the C. sabulosa chloroplast (cp.) genome. The study results showed that the genome was 156,488 bp in length. It had a quadripartite structure consisting of two inverted repeats (IRb and IRa) of 24,649-bp, separated by an 87,696-bp LSC region and a 19,494-bp SSC region. The CP genome contained 113 unique genes, including four rRNA genes, 30 tRNA genes, and 79 CDS genes. In the second copy of the inverted repeat, there were 18 duplicated genes. The C. sabulosa lacks the petD, petB, rpl2, and rps16 intron. The analysis of simple sequence repeats (SSRs) revealed 93 SSR loci of 22 types and 78 oligonucleotide repeats of four kinds. The phylogenetic investigation showed that the Chrozophora genus evolved paraphyletically from other members of the Euphorbiaceae family. To support the phylogenetic findings, we selected species from the Euphorbiaceae and Phyllanthaceae families to compare with C. sabulosa for Ks and Ka substitution rates, InDels investigation, IR contraction and expansion, and SNPs analysis. The results of these comparative studies align with the phylogenetic findings. We identified six highly polymorphic regions shared by both families, which could be used as molecular identifiers for the Chrozophora genus (rpl33-rps18, rps18-rpl20, rps15-ycf1, ndhG-ndhI, psaI-ycf4, petA-psbJ). The cp. genome sequence of C. sabulosa reveals the evolution of plastid sequences in Chrozophora species. This is the first time the cp. genome of a Chrozophora genus has been sequenced, serving as a foundation for future sequencing of other species within the Chrozophoreae tribe and facilitating in-depth taxonomic research. The results of this research will also aid in identifying new Chrozophora species.
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Affiliation(s)
- Nida Javaid
- The Islamia University, Bahawalpur, Pakistan
| | | | | | - Yanjun Du
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs,School of Rural Revitalization), Hainan University, Haikou, P.R. China
| | - Muhammad Anwar
- School of Tropical Agriculture and Forestry (School of Agriculture and Rural Affairs,School of Rural Revitalization), Hainan University, Haikou, P.R. China.
- Key Laboratory of Genetic and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou, P.R. China.
- , Haikou, P.R. China.
| | - Song Xiqiang
- Key Laboratory of Genetic and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Haikou, P.R. China.
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Xu Y, Li Y, Chen Y, Wang L, Xue B, Zhang X, Song W, Guo W, Wu W. Comparative Analysis of Complete Chloroplast Genomes of Rubus in China: Hypervariable Regions and Phylogenetic Relationships. Genes (Basel) 2024; 15:716. [PMID: 38927652 PMCID: PMC11202638 DOI: 10.3390/genes15060716] [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: 04/23/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
With more than 200 species of native Rubus, China is considered a center of diversity for this genus. Due to a paucity of molecular markers, the phylogenetic relationships for this genus are poorly understood. In this study, we sequenced and assembled the plastomes of 22 out of 204 Chinese Rubus species (including varieties) from three of the eight sections reported in China, i.e., the sections Chamaebatus, Idaeobatus, and Malachobatus. Plastomes were annotated and comparatively analyzed with the inclusion of two published plastomes. The plastomes of all 24 Rubus species were composed of a large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs), and ranged in length from 155,464 to 156,506 bp. We identified 112 unique genes, including 79 protein-coding genes, 29 transfer RNAs, and four ribosomal RNAs. With highly consistent gene order, these Rubus plastomes showed strong collinearity, and no significant changes in IR boundaries were noted. Nine divergent hotspots were identified based on nucleotide polymorphism analysis: trnH-psbA, trnK-rps16, rps16-trnQ-psbK, petN-psbM, trnT-trnL, petA-psbJ, rpl16 intron, ndhF-trnL, and ycf1. Based on whole plastome sequences, we obtained a clearer phylogenetic understanding of these Rubus species. All sampled Rubus species formed a monophyletic group; however, sections Idaeobatus and Malachobatus were polyphyletic. These data and analyses demonstrate the phylogenetic utility of plastomes for systematic research within Rubus.
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Affiliation(s)
- Yufen Xu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
| | - Yongquan Li
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Yanzhao Chen
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Longyuan Wang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Bine Xue
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Xianzhi Zhang
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wenpei Song
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
| | - Wei Wu
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (Y.X.); (Y.L.); (Y.C.); (L.W.); (B.X.); (X.Z.); (W.S.); (W.W.)
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Makhmudjanov D, Volis S, Yusupov Z, Juramurodov I, Tojibaev K, Deng T, Sun H. Central Asia revealed as a key area in evolution of Eremurus (Asphodelaceae). PLANT DIVERSITY 2024; 46:333-343. [PMID: 38798731 PMCID: PMC11119512 DOI: 10.1016/j.pld.2023.08.004] [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: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 05/29/2024]
Abstract
Eremurus was described at the beginning of the 19th century. However, due to limited sampling and the small number of gene markers to date, its phylogeny and evolution are largely unknown. In this study, we analyzed plastomes from 27 species belonging to 2 subgenera and 3 sections of Eremurus, which are found in Central Asia (its center of diversity) and China. We also analyzed nuclear DNA ITS of 33 species, encompassing all subgenera and sections of the genus in Central Asia, southwest Asia and China. Our findings revealed that the genus was monophyletic, although both subgenera Eremurus and Henningia were found to be paraphyletic. Both plastome and nrDNA-based phylogenetic trees had three clades that did not reflect the current taxonomy of the genus. Our biogeographical and time-calibrated trees suggest that Eremurus originated in the ancient Tethyan area in the second half of the Eocene. Diversification of Eremurus occurred from the early Oligocene to the late Miocene. Paratethys Sea retreat and several orogenetic events, such as the progressive uplift of the Qinghai-Tibet Plateau and surrounding mountain belts (Altai, Pamir, Tian Shan), caused serious topographic and climate (aridification) changes in Central Asia that may have triggered a split of clades and speciation. In this transformed Central Asia, speciation proceeded rapidly driven mainly by vicariance caused by numerous mountain chains and specialization to a variety of climatic, topographic and soil conditions that exist in this region.
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Affiliation(s)
- Dilmurod Makhmudjanov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Sergei Volis
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Ziyoviddin Yusupov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Inom Juramurodov
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Komiljon Tojibaev
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent 100125, Uzbekistan
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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Wu H, Li DZ, Ma PF. Unprecedented variation pattern of plastid genomes and the potential role in adaptive evolution in Poales. BMC Biol 2024; 22:97. [PMID: 38679718 PMCID: PMC11057118 DOI: 10.1186/s12915-024-01890-5] [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: 07/27/2023] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND The plastid is the photosynthetic organelle in plant cell, and the plastid genomes (plastomes) are generally conserved in evolution. As one of the most economically and ecologically important order of angiosperms, Poales was previously documented to exhibit great plastomic variation as an order of photoautotrophic plants. RESULTS We acquired 93 plastomes, representing all the 16 families and 5 major clades of Poales to reveal the extent of their variation and evolutionary pattern. Extensive variation including the largest one in monocots with 225,293 bp in size, heterogeneous GC content, and a wide variety of gene duplication and loss were revealed. Moreover, rare occurrences of three inverted repeat (IR) copies in angiosperms and one IR loss were observed, accompanied by short IR (sIR) and small direct repeat (DR). Widespread structural heteroplasmy, diversified inversions, and unusual genomic rearrangements all appeared in Poales, occasionally within a single species. Extensive repeats in the plastomes were found to be positively correlated with the observed inversions and rearrangements. The variation all showed a "small-large-moderate" trend along the evolution of Poales, as well as for the sequence substitution rate. Finally, we found some positively selected genes, mainly in C4 lineages, while the closely related lineages of those experiencing gene loss tended to have undergone more relaxed purifying selection. CONCLUSIONS The variation of plastomes in Poales may be related to its successful diversification into diverse habitats and multiple photosynthetic pathway transitions. Our order-scale analyses revealed unusual evolutionary scenarios for plastomes in the photoautotrophic order of Poales and provided new insights into the plastome evolution in angiosperms as a whole.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species and Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Chen S, Safiul Azam FM, Akter ML, Ao L, Zou Y, Qian Y. The first complete chloroplast genome of Thalictrum fargesii: insights into phylogeny and species identification. FRONTIERS IN PLANT SCIENCE 2024; 15:1356912. [PMID: 38745930 PMCID: PMC11092384 DOI: 10.3389/fpls.2024.1356912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Introduction Thalictrum fargesii is a medicinal plant belonging to the genus Thalictrum of the Ranunculaceae family and has been used in herbal medicine in the Himalayan regions of China and India. This species is taxonomically challenging because of its morphological similarities to other species within the genus. Thus, herbal drugs from this species are frequently adulterated, substituted, or mixed with other species, thereby endangering consumer safety. Methods The present study aimed to sequence and assemble the entire chloroplast (cp) genome of T. fargesii using the Illumina HiSeq 2500 platform to better understand the genomic architecture, gene composition, and phylogenetic relationships within the Thalictrum. Results and discussion The cp genome was 155,929 bp long and contained large single-copy (85,395 bp) and small single-copy (17,576 bp) regions that were segregated by a pair of inverted repeat regions (26,479 bp) to form a quadripartite structure. The cp genome contains 133 genes, including 88 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes. Additionally, this genome contains 64 codons that encode 20 amino acids, the most preferred of which are alanine and leucine. We identified 68 SSRs, 27 long repeats, and 242 high-confidence C-to-U RNA-editing sites in the cp genome. Moreover, we discovered seven divergent hotspot regions in the cp genome of T. fargesii, among which ndhD-psaC and rpl16-rps3 may be useful for developing molecular markers for identifying ethnodrug species and their contaminants. A comparative study with eight other species in the genus revealed that pafI and rps19 had highly variable sites in the cp genome of T. fargesii. Additionally, two special features, (i) the shortest length of the ycf1 gene at the IRA-SSC boundary and (ii) the distance between the rps19 fragment and trnH at the IRA-LSC junction, distinguish the cp genome of T. fargesii from those of other species within the genus. Furthermore, phylogenetic analysis revealed that T. fargesii was closely related to T. tenue and T. petaloidium. Conclusion Considering all these lines of evidence, our findings offer crucial molecular and evolutionary information that could play a significant role in further species identification, evolution, and phylogenetic studies on T. fargesii.
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Affiliation(s)
- Shixi Chen
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Fardous Mohammad Safiul Azam
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Mst. Lovely Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, University of Development Alternative, Dhaka, Bangladesh
| | - Li Ao
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Key Laboratory of Regional Characteristic Agricultural Resources, College of Life Sciences, Neijiang Normal University, Neijiang, Sichuan, China
| | - Yuanchao Zou
- College of Life Science, Neijiang Normal University, Neijiang, Sichuan, China
- Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Key Laboratory of Sichuan Province, Neijiang Normal University, Sichuan, China
| | - Ye Qian
- Branch of The First Affiliated Hospital of Xinjiang Medical University, Changji, Xinjiang, China
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Han S, Zhang S, Yi R, Bi D, Ding H, Yang J, Ye Y, Xu W, Wu L, Zhuo R, Kan X. Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae). ANNALS OF BOTANY 2024; 133:585-604. [PMID: 38359907 PMCID: PMC11037489 DOI: 10.1093/aob/mcae017] [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: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND AND AIMS Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes. METHODS To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes). KEY RESULTS Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic. CONCLUSIONS This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.
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Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ran Yi
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Hengwu Ding
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jianke Yang
- School of Basic Medical Sciences, Wannan Medical College, Wuhu 241000, China
| | - Yuanxin Ye
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longhua Wu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Jia L, Wang S, Hu J, Miao K, Huang Y, Ji Y. Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales. BMC PLANT BIOLOGY 2024; 24:277. [PMID: 38605351 PMCID: PMC11010409 DOI: 10.1186/s12870-024-04917-9] [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: 10/10/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence. RESULTS Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. CONCLUSIONS Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.
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Affiliation(s)
- Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Seo YS, Song JH, Kim HS, Nam HH, Yang S, Choi G, Chae SW, Lee J, Jung B, Kim JS, Park I. An Integrative Study of Scrophularia takesimensis Nakai in an Ovalbumin-Induced Murine Model of Asthma: The Effect on T Helper 2 Cell Activation. Pharmaceutics 2024; 16:529. [PMID: 38675190 PMCID: PMC11055152 DOI: 10.3390/pharmaceutics16040529] [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: 01/18/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Scrophularia have traditionally been used as herbal medicines to treat neuritis, sore throats, and laryngitis. In particular, S. takesimensis, a Korean endemic species with restricted distribution on Ulleung Island, holds significant resource and genetic value. However, its pharmacological properties have not been thoroughly evaluated. Thus, we provide detailed morphological characteristics and genomic information for S. takesimensis in this study. Moreover, its pharmacological activity was evaluated in an ovalbumin-induced asthma rat model, using extracts of S. takesimensis roots (100 or 200 mg/kg). The distinguishing features of S. takesimensis from related species include the presence or absence of stem wings, leaf shape, and habitat. The chloroplast (cp) genome of this species is 152,420 bp long and exhibits a conserved quadripartite structure. A total of 114 genes were identified, which included 80 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. The gene order, content, and orientation of the S. takesimensis cp genome was highly conserved and consistent with the general structure observed in S. buergeriana and S. ningpoensis cp genomes. Confirming the anti-inflammatory effects of S. takesimensis extract (STE) using an established mouse model of ovalbumin-induced asthma, we observed reduced asthmatic phenotypes, including inflammatory cell infiltration, mucus production, and suppression of T helper 2 (Th2) cell. Furthermore, STE treatment reduced Th2 cell activation and differentiation. This study underscores the medicinal value of S. takesimensis. The importance of preserving S. takesimensis was revealed and crucial insights were provided for further research on its utilization as a medicinal resource.
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Affiliation(s)
- Yun-Soo Seo
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (Y.-S.S.); (H.S.K.); (H.H.N.); (S.Y.); (G.C.)
- Center for Companion Animal New Drug Development, Jeonbuk Branch, Korea Institute of Toxicology, Jeongeup 56212, Republic of Korea;
| | - Jun-Ho Song
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea;
| | - Hyo Seon Kim
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (Y.-S.S.); (H.S.K.); (H.H.N.); (S.Y.); (G.C.)
| | - Hyeon Hwa Nam
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (Y.-S.S.); (H.S.K.); (H.H.N.); (S.Y.); (G.C.)
- Center for Companion Animal New Drug Development, Jeonbuk Branch, Korea Institute of Toxicology, Jeongeup 56212, Republic of Korea;
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (Y.-S.S.); (H.S.K.); (H.H.N.); (S.Y.); (G.C.)
| | - Goya Choi
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju 58245, Republic of Korea; (Y.-S.S.); (H.S.K.); (H.H.N.); (S.Y.); (G.C.)
| | - Sung-Wook Chae
- Center for Companion Animal New Drug Development, Jeonbuk Branch, Korea Institute of Toxicology, Jeongeup 56212, Republic of Korea;
- KM Convergence Research Division, Korea Institute of Oriental Medicine, 1672 Yuseongdae-ro, Yuseong-gu, Daejeon 34054, Republic of Korea
| | - Jeongmin Lee
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (J.L.); (B.J.)
| | - Bokyung Jung
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (J.L.); (B.J.)
| | - Joong-Sun Kim
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, Republic of Korea; (J.L.); (B.J.)
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon 51140, Republic of Korea
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Sun W, Wei Z, Gu Y, Wang T, Liu B, Yan Y. Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region. FRONTIERS IN PLANT SCIENCE 2024; 15:1328080. [PMID: 38665369 PMCID: PMC11044155 DOI: 10.3389/fpls.2024.1328080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/02/2024] [Indexed: 04/28/2024]
Abstract
Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.
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Affiliation(s)
- Weiyue Sun
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Zuoying Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Yuefeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Ting Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Baodong Liu
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
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11
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Friis EM, Crane PR, Pedersen KR, Marone F. Cretaceous chloranthoids: early prominence, extinct diversity and missing links. ANNALS OF BOTANY 2024; 133:225-260. [PMID: 38597914 PMCID: PMC11005782 DOI: 10.1093/aob/mcad137] [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: 05/01/2023] [Accepted: 09/07/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND The Chloranthaceae comprise four extant genera (Hedyosmum, Ascarina, Chloranthus and Sarcandra), all with simple flowers. Molecular phylogenetics indicates that the Chloranthaceae diverged very early in angiosperm evolution, although how they are related to eudicots, magnoliids, monocots and Ceratophyllum is uncertain. Fossil pollen similar to that of Ascarina and Hedyosmum has long been recognized in the Early Cretaceous, but over the last four decades evidence of extinct Chloranthaceae based on other types of fossils has expanded dramatically and contributes significantly to understanding the evolution of the family. SCOPE Studies of fossils from the Cretaceous, especially mesofossils of Early Cretaceous age from Portugal and eastern North America, recognized diverse flowers, fruits, seeds, staminate inflorescences and stamens of extinct chloranthoids. These early chloranthoids include forms related to extant Hedyosmum and also to the Ascarina, Chloranthus and Sarcandra clade. In the Late Cretaceous there are several occurrences of distinctive fossil androecia related to extant Chloranthus. The rich and still expanding Cretaceous record of Chloranthaceae contrasts with a very sparse Cenozoic record, emphasizing that the four extant genera are likely to be relictual, although speciation within the genera might have occurred in relatively recent times. In this study, we describe three new genera of Early Cretaceous chloranthoids and summarize current knowledge on the extinct diversity of the group. CONCLUSIONS The evolutionary lineage that includes extant Chloranthaceae is diverse and abundantly represented in Early Cretaceous mesofossil floras that provide some of the earliest evidence of angiosperm reproductive structures. Extinct chloranthoids, some of which are clearly in the Chloranthaceae crown group, fill some of the morphological gaps that currently separate the extant genera, help to illuminate how some of the unusual features of extant Chloranthaceae evolved and suggest that Chloranthaceae are of disproportionate importance for a more refined understanding of ecology and phylogeny of early angiosperm diversification.
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Affiliation(s)
- Else Marie Friis
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Peter R Crane
- Oak Spring Garden Foundation, 1776 Loughborough Lane, Upperville, VA 20184, USA
- Yale School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Kaj Raunsgaard Pedersen
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
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12
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Yaradua SS, Yessoufou K. Chloroplast genome of Ecbolium viride (Forssk.) Alston: plastome evolution and phylogenomics of Justiceae (Acanthaceae, Acanthoideae). Genome 2024. [PMID: 38593472 DOI: 10.1139/gen-2024-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Justicieae is the most taxonomically complex tribe in Acanthaceae. Here, we sequenced the plastome of Ecbolium viride, a medicinally important species. The genome was analyzed with previously reported plastome of Justiceae. The plastome of E. viride has quadripartite structure with a length of 151 185 bp. The comparative genomic analyses revealed no structural inversion in Justiceae and some regions (rpoC2, ycf2, ycf1, ndhH rps16-trnQ-UGG, and trnL-CAA-ycf15) exhibiting a significant level of nucleotide divergence. The positive selection analyses revealed that some species in the tribe have undergone adaptive evolution. The visualization of the boundaries between the single copy and inverted repeat regions revealed that Justiceae chloroplast genome experienced some levels of variation, which give an insight into the evolution of the species. The longest genome was in the earliest diverged taxa of the tribe Pseuderanthemum haikangense and from this genome, a series of contraction and expansion occurred contributing to the evolution of other lineages. The plastome-based phylogeny revealed and confirmed the monophyly of Justiceae, polyphyly of Justicia and supported the tribal classification Graptophyllinae, Tetrameriinae, and Isoglossinae. We proposed that Declipterinae should be treated as subtribe and the status of Justiciinae can only be confirmed after the resolution of the polyphyletic Justicia.
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Affiliation(s)
- Samaila Samaila Yaradua
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, APK Campus, University of Johannesburg, Johannesburg 2006, South Africa
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13
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Liu L, Li H, Li J, Li X, Hu N, Sun J, Zhou W. Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis. BMC PLANT BIOLOGY 2024; 24:254. [PMID: 38594633 PMCID: PMC11003120 DOI: 10.1186/s12870-024-04979-9] [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: 11/20/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. RESULTS The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens. CONCLUSIONS The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.
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Affiliation(s)
- LiE Liu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - HongYan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - JiaXin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - XinJuan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China.
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14
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Choi TY, Lee SR. Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes. PLoS One 2024; 19:e0301346. [PMID: 38578735 PMCID: PMC10997070 DOI: 10.1371/journal.pone.0301346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/14/2024] [Indexed: 04/07/2024] Open
Abstract
Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.
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Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, Chosun University, Gwangju, South Korea
| | - Soo-Rang Lee
- Department of Biology Education, Chosun University, Gwangju, South Korea
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15
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Li T, Zhang S, Deng Y, Li Y. Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution. Genes (Basel) 2024; 15:406. [PMID: 38674341 PMCID: PMC11048997 DOI: 10.3390/genes15040406] [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: 02/28/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Manglietia Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of Manglietia using plastid genetic information. We newly sequenced the complete or nearly complete plastomes of four Manglietia species (Manglietia aromatica, Manglietia calcarea, Manglietia kwangtungensis, and Manglietia glauca) and conducted comparative analysis with seventeen published plastomes to examine the evolutionary pattern within this genus. The plastomes of these five newly sequenced Manglietia species range from 157,093 bp (M. calcarea2) to 160,493 bp (M. kwangtungensis), all exhibiting circular structures when mapped. Nucleotide diversity was observed across the plastomes, leading us to identify 13 mutational hotspot regions, comprising eight intergenic spacer regions and five gene regions. Our phylogenetic analyses based on 77 protein-coding genes generated phylogenetic relationships with high support and resolution for Manglietia. This genus can be divided into three clades, and the previously proposed infrageneric classifications are not supported by our studies. Furthermore, the close affinity between M. aromatica and M. calcarea is supported by the present work, and further studies are necessary to conclude the taxonomic treatment for the latter. These results provide resources for the comparative plastome, breeding, and plastid genetic engineering of Magnoliaceae and flowering plants.
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Affiliation(s)
- Tingzhang Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (T.L.); (S.Z.)
| | - Shuangyu Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (T.L.); (S.Z.)
| | - Yunfei Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yuling Li
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (T.L.); (S.Z.)
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16
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Lu R, Hu K, Sun X, Chen M. Low-coverage whole genome sequencing of diverse Dioscorea bulbifera accessions for plastome resource development, polymorphic nuclear SSR identification, and phylogenetic analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1373297. [PMID: 38510439 PMCID: PMC10950973 DOI: 10.3389/fpls.2024.1373297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Dioscorea bulbifera (Dioscoreaceae), a versatile herbaceous climber native to Africa and Asia, holds significant nutritional and medicinal value. Despite extensive characterization and genetic variability analyses of African accessions, studies on the genetic variation of this species in China are limited. To address this gap, we conducted low-coverage whole genome sequencing on D. bulbifera accessions from diverse regions across mainland China and Taiwan island. Our initial investigation encompassed comprehensive comparative plastome analyses of these D. bulbifera accessions, and developing plastome resources (including plastome-derived repetitive sequences, SSRs, and divergent hotspots). We also explored polymorphic nuclear SSRs and elucidated the intraspecific phylogeny of these accessions. Comparative plastome analyses revealed that D. bulbifera plastomes exhibited a conserved quadripartite structure with minimal size variation mainly attributed to intergenic spacer regions, reinforcing prior observations of a high degree of conservation within a species. We identified 46 to 52 dispersed repeats and 151 to 163 plastome-derived SSRs, as well as highlighted eight key divergent hotspots in these D. bulbifera accessions. Furthermore, we developed 2731 high-quality candidate polymorphic nuclear SSRs for D. bulbifera. Intraspecific phylogenetic analysis revealed three distinct clades, where accessions from Southeast China formed a sister group to those from South China and Taiwan island, and collectively, these two clades formed a sister group to the remaining accessions, indicating potential regional genetic divergence. These findings not only contributed to the understanding of the genetic variation of D. bulbifera, but also offered valuable resources for future research, breeding efforts, and utilization of this economically important plant species.
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Affiliation(s)
- Ruisen 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
| | - 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
| | - Xiaoqin 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
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17
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Zhou N, Miao K, Liu C, Jia L, Hu J, Huang Y, Ji Y. Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics. PLANT DIVERSITY 2024; 46:219-228. [PMID: 38807906 PMCID: PMC11128834 DOI: 10.1016/j.pld.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 05/30/2024]
Abstract
Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.
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Affiliation(s)
- Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changkun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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18
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Nyamgerel N, Baasanmunkh S, Oyuntsetseg B, Tsegmed Z, Bayarmaa GA, Lazkov G, Pyak E, Gil HY, Park I, Choi HJ. Comparative plastome analysis and taxonomic classification of snow lotus species (Saussurea, Asteraceae) in Central Asia and Southern Siberia. Funct Integr Genomics 2024; 24:42. [PMID: 38396290 PMCID: PMC10891264 DOI: 10.1007/s10142-024-01309-y] [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: 12/24/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Four species of Saussurea, namely S. involucrata, S. orgaadayi, S. bogedaensis, and S. dorogostaiskii, are known as the "snow lotus," which are used as traditional medicines in China (Xinjiang), Kyrgyzstan, Mongolia, and Russia (Southern Siberia). These species are threatened globally, because of illegal harvesting and climate change. Furthermore, the taxonomic classification and identification of these threatened species remain unclear owing to limited research. The misidentification of medicinal species can sometimes be harmful to health. Therefore, the phylogenetic and genomic features of these species need to be confirmed. In this study, we sequenced five complete chloroplast genomes and seven nuclear ITS regions of four snow lotus species and other Saussurea species. We further explored their genetic variety, selective pressure at the sequence level, and phylogenetic relationships using the chloroplast genome, nuclear partial DNA sequences, and morphological features. Plastome of the snow lotus species has a conserved structure and gene content similar to most Saussurea species. Two intergenic regions (ndhJ-ndhK and ndhD-psaC) show significantly high diversity among chloroplast regions. Thus, ITS and these markers are suitable for identifying snow lotus species. In addition, we characterized 43 simple sequence repeats that may be useful in future population genetic studies. Analysis of the selection signatures identified three genes (rpoA, ndhB, and ycf2) that underwent positive selection. These genes may play important roles in the adaptation of the snow lotus species to alpine environments. S. dorogostaiskii is close to S. baicalensis and exhibits slightly different adaptation from others. The taxonomic position of the snow lotus species, confirmed by morphological and molecular evidence, is as follows: (i) S. involucrata has been excluded from the Mongolian flora due to misidentification as S. orgaadayi or S. bogedaensis for a long time; (ii) S. dorogostaiskii belongs to section Pycnocephala subgenus Saussurea, whereas other the snow lotus species belong to section Amphilaena subgenus Amphilaena; and (iii) S. krasnoborovii is synonymous of S. dorogostaiskii. This study clarified the speciation and lineage diversification of the snow lotus species in Central Asia and Southern Siberia.
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Affiliation(s)
- Nudkhuu Nyamgerel
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea
| | | | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Zagarjav Tsegmed
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea
| | - Gun-Aajav Bayarmaa
- Department of Biology, School of Arts and Science, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Georgy Lazkov
- Institute for Biology, National Academy of Sciences, Bishkek, Kyrgyzstan
| | - Elizaveta Pyak
- Department of Botany, Tomsk State University, Tomsk, Russia
| | - Hee-Young Gil
- Department of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Korea
| | - Inkyu Park
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea.
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea.
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Wang H, Zhang Y, Zhang L, Wang J, Guo H, Zong J, Chen J, Li D, Li L, Liu J, Li J. Molecular Characterization and Phylogenetic Analysis of Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence. Curr Issues Mol Biol 2024; 46:1635-1650. [PMID: 38392224 PMCID: PMC10888139 DOI: 10.3390/cimb46020106] [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: 01/08/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.
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Affiliation(s)
- Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
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20
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Lubna, Asaf S, Jan R, Asif S, Bilal S, Khan AL, Al-Rawahi AN, Kim KM, Al-Harrasi A. The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis. Sci Rep 2024; 14:4006. [PMID: 38369569 PMCID: PMC10874969 DOI: 10.1038/s41598-024-54503-0] [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: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.
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Affiliation(s)
- Lubna
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - 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 Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Ahmed N Al-Rawahi
- Natural and Medical Sciences 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 Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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21
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Cao J, Wang H, Cao Y, Kan S, Li J, Liu Y. Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats. Int J Mol Sci 2024; 25:2278. [PMID: 38396955 PMCID: PMC10888665 DOI: 10.3390/ijms25042278] [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: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.
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Affiliation(s)
- Jialiang Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China;
| | - Jiamei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanyan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
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22
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Liu L, Li H, Li J, Li X, Hu N, Wang H, Zhou W. Chloroplast genome analyses of Caragana arborescens and Caragana opulens. BMC Genom Data 2024; 25:16. [PMID: 38336648 PMCID: PMC10854190 DOI: 10.1186/s12863-024-01202-4] [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: 06/08/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Numerous species within the genus Caragana have high ecological and medicinal value. However, species identification based on morphological characteristics is quite complicated in the genus. To address this issue, we analyzed complete plastid genome data for the genus. RESULTS We obtained chloroplast genomes of two species, Caragana arborescens and Caragana opulens, using Illumina sequencing technology, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species indicated that they could be assigned to the inverted repeat-lacking clade (IRLC). The genomes included 111 distinct genes (4 rRNA genes, 31 tRNA genes, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in the two genomes, the majority of which contained a single intron. Repeat analyses revealed 129 and 229 repeats in C. arborescens and C. opulens, respectively. C. arborescens and C. opulens genomes contained 277 and 265 simple sequence repeats, respectively. The two Caragana species exhibited similar codon usage patterns. rpl20-clpP, rps19-rpl2, and rpl23-ycf2 showed the highest nucleotide diversity (pi). In an analysis of sequence divergence, certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) were highly variable. A phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together with four other Caragana species. The genera Astragalus and Caragana were relatively closely related. CONCLUSIONS The present study provides valuable information about the chloroplast genomes of C. arborescens and C. opulens and lays a foundation for future phylogenetic research and molecular marker development.
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Affiliation(s)
- LiE Liu
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Hongyan Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Jiaxin Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Xinjuan Li
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Honglun Wang
- Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- School of Ecological and Environmental Engineering, Qinghai University, Xining, 810016, China.
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Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [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: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
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Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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24
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Marczuk-Rojas JP, Álamo-Sierra AM, Salmerón A, Alcayde A, Isanbaev V, Carretero-Paulet L. Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome of Moringa oleifera reveals unanticipated complexity in NUPTs´ formation. BMC Genomics 2024; 25:60. [PMID: 38225585 PMCID: PMC10789010 DOI: 10.1186/s12864-024-09979-5] [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: 06/26/2023] [Accepted: 01/06/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. RESULTS Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. CONCLUSIONS Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.
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Affiliation(s)
- Juan Pablo Marczuk-Rojas
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Angélica María Álamo-Sierra
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Antonio Salmerón
- Department of Mathematics, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Alfredo Alcayde
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Viktor Isanbaev
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain.
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
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25
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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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Xue TT, Janssens SB, Liu BB, Yu SX. Phylogenomic conflict analyses of the plastid and mitochondrial genomes via deep genome skimming highlight their independent evolutionary histories: A case study in the cinquefoil genus Potentilla sensu lato (Potentilleae, Rosaceae). Mol Phylogenet Evol 2024; 190:107956. [PMID: 37898296 DOI: 10.1016/j.ympev.2023.107956] [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: 07/24/2023] [Revised: 09/28/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigate phylogenetic conflict analyses within and between plastid and mitochondrial genomes using Potentilla as a case study. We generated three plastid datasets (coding, noncoding, and all-region) and one mitochondrial dataset (coding regions) to infer phylogenies based on concatenated and multispecies coalescent (MSC) methods. Conflict analyses were then performed using PhyParts and Quartet Sampling (QS). Both plastid and mitochondrial genomes divided the Potentilla into eight highly supported clades, two of which were newly identified in this study. While most organellar loci were uninformative for the majority of nodes (bootstrap value < 70%), PhyParts and QS detected conflicting signals within the two organellar genomes. Regression analyses revealed that conflict signals mainly occurred among shorter loci, whereas longer loci tended to be more concordant with the species tree. In addition, two significant disagreements between the two organellar genomes were detected, likely attributed to hybridization and/or incomplete lineage sorting. Our results demonstrate that mitochondrial genes can fully resolve the phylogenetic relationships among eight major clades of Potentilla and are not always linked with plastome in evolutionary history. Stochastic inferences appear to be the primary source of observed conflicts among the gene trees. We recommend that the loci with short sequence length or containing limited informative sites should be used cautiously in MSC analysis, and suggest the joint application of concatenated and MSC methods for phylogenetic inference using organellar genomes.
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Affiliation(s)
- Tian-Tian Xue
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium; Department of Biology, KU Leuven, Kasteelpark Arenberg 31, BE-3001 Leuven, Belgium.
| | - Bin-Bin Liu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Sheng-Xiang Yu
- State Key Laboratory of Plant Diversity and Specialty Crops / State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Javaid N, Ramzan M, Jabeen S, Shah MN, Danish S, Hirad AH. Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan. BMC PLANT BIOLOGY 2023; 23:658. [PMID: 38124056 PMCID: PMC10731703 DOI: 10.1186/s12870-023-04670-5] [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: 07/07/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides. RESULTS The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ. CONCLUSION The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.
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Affiliation(s)
- Nida Javaid
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan
| | - Musarrat Ramzan
- Department of Botany, Faculty of Chemical and Biological Sciences, The Islamia University Bahawalpur, Bahawalpur, Punjab, Pakistan.
| | - Shagufta Jabeen
- Government Associate College for Women Ahmedpur East, Bahawalpur, Punjab, Pakistan
| | - Muhammad Nadeem Shah
- Department of Agriculture, Government College University Lahore, Lahore, Punjab, Pakistan
- North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, Florida, USA
| | - Subhan Danish
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, Punjab, Pakistan.
| | - Abdurahman Hajinur Hirad
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. Box.2455, Riyadh, 11451, Saudi Arabia
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Yang Q, Xin C, Xiao QS, Lin YT, Li L, Zhao JL. Codon usage bias in chloroplast genes implicate adaptive evolution of four ginger species. FRONTIERS IN PLANT SCIENCE 2023; 14:1304264. [PMID: 38169692 PMCID: PMC10758403 DOI: 10.3389/fpls.2023.1304264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Codon usage bias (CUB) refers to different codons exhibiting varying frequencies of usage in the genome. Studying CUB is crucial for understanding genome structure, function, and evolutionary processes. Herein, we investigated the codon usage patterns and influencing factors of protein-coding genes in the chloroplast genomes of four sister genera (monophyletic Roscoea and Cautleya, and monophyletic Pommereschea and Rhynchanthus) from the Zingiberaceae family with contrasting habitats in southwestern China. These genera exhibit distinct habitats, providing a unique opportunity to explore the adaptive evolution of codon usage. We conducted a comprehensive analysis of nucleotide composition and codon usage on protein-coding genes in the chloroplast genomes. The study focused on understanding the relationship between codon usage and environmental adaptation, with a particular emphasis on genes associated with photosynthesis. Nucleotide composition analysis revealed that the overall G/C content of the coding genes was ˂ 48%, indicating an enrichment of A/T bases. Additionally, synonymous and optimal codons were biased toward ending with A/U bases. Natural selection is the primary factor influencing CUB characteristics, particularly photosynthesis-associated genes. We observed differential gene expressions related to light adaptation among sister genera inhabiting different environments. Certain codons were favored under specific conditions, possibly contributing to gene expression regulation in particular environments. This study provides insights into the adaptive evolution of these sister genera by analyzing CUB and offers theoretical assistance for understanding gene expression and regulation. In addition, the data support the relationship between RNA editing and CUB, and the findings shed light on potential research directions for investigating adaptive evolution.
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Affiliation(s)
- Qian Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Cheng Xin
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qing-Song Xiao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Ya-Ting Lin
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Li Li
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
| | - Jian-Li Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Centre for Invasion Biology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, China
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Krawczyk K, Paukszto Ł, Maździarz M, Sawicki J. The low level of plastome differentiation observed in some lineages of Poales hinders molecular species identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1275377. [PMID: 38143577 PMCID: PMC10739336 DOI: 10.3389/fpls.2023.1275377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023]
Abstract
Chloroplast genomes are a source of information successfully used in various fields of plant genetics, including molecular species identification. However, recent studies indicate an extremely low level of interspecific variability in the plastomes of some taxonomic groups of plants, including the genus Stipa L., which is a representative of the grass family. In this study we aimed to analyze the level of chloroplast genome diversity within particular genera as well as the effectiveness of identifying plant species in the Poaceae family and the other representatives of Poales order. Analysis of complete plastid genome alignments created for 96 genera comprising 793 species and 1707 specimens obtained from the GenBank database allowed defining and categorizing molecular diagnostic characters distinguishing the analyzed species from the other representatives of the genus. The results also demonstrate which species do not have any species-specific mutations, thereby they cannot be identified on the basis of differences between the complete chloroplast genomes. Our research showed a huge diversity of the analyzed species in terms of the number of molecular diagnostic characters and indicated which genera pose a particular challenge in terms of molecular species identification. The results show that a very low level of genetic diversity between plastomes is not uncommon in Poales. This is the first extensive research on super-barcoding that tests this method on a large data set and illustrates its effectiveness against the background of phylogenetic relationships.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Milarska SE, Androsiuk P, Paukszto Ł, Jastrzębski JP, Maździarz M, Larson KW, Giełwanowska I. Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis. Sci Rep 2023; 13:18774. [PMID: 37907682 PMCID: PMC10618263 DOI: 10.1038/s41598-023-46017-y] [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: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023] Open
Abstract
The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.
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Affiliation(s)
- Sylwia E Milarska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Piotr Androsiuk
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Jan P Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Mateusz Maździarz
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Pl. Łódzki 1, 10-721, Olsztyn, Poland
| | - Keith W Larson
- Climate Impacts Research Centre, Umeå University, 90187, Umeå, Sweden
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, ul. M. Oczapowskiego 1A, 10-719, Olsztyn, Poland
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Shang M, Wang J, Dai G, Zheng J, Liao B, Wang J, Duan B. Comparative analysis of chloroplast genome and new insights into phylogenetic relationships of Ajuga and common adulterants. FRONTIERS IN PLANT SCIENCE 2023; 14:1251829. [PMID: 37954994 PMCID: PMC10634298 DOI: 10.3389/fpls.2023.1251829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Introduction The potential contamination of herbal medicinal products poses a significant concern for consumer health. Given the limited availability of genetic information concerning Ajuga species, it becomes imperative to incorporate supplementary molecular markers to enhance and ensure accurate species identification. Methods In this study, the chloroplast (cp) genomes of seven species of the genus Ajuag were sequenced, de novo assembled and characterized. Results exhibiting lengths ranging from 150,342 bp to 150,472 bp, encompassing 86 - 88 protein-coding genes (PCGs), 35 - 37 transfer RNA, and eight ribosomal RNA. The repetitive sequences, codon uses, and cp genomes of seven species were highly conserved, and PCGs were the reliable molecular markers for investigating the phylogenetic relationship within the Ajuga genus. Moreover, four mutation hotspot regions (accD-psaI, atpH-atpI, ndhC-trnV(UAC), and ndhF-rpl23) were identified within cp genomes of Ajuga, which could help distinguish A. bracteosa and its contaminants. Based on cp genomes and PCGs, the phylogenetic tree preliminary confirmed the position of Ajuga within the Lamiaceae family. It strongly supported a sister relationship between Subsect. Genevense and Subsect. Biflorae, suggesting the merger of Subsect. Biflorae and Subsect. Genevenses into one group rather than maintaining separate categorizations. Additionally, molecular clock analysis estimated the divergence time of Ajuga to be around 7.78 million years ago. Discussion The species authentication, phylogeny, and evolution analyses of the Ajuga species may benefit from the above findings.
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Affiliation(s)
- Mingyue Shang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiale Wang
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guona Dai
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jiamei Zheng
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Binbin Liao
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jing Wang
- College of Pharmaceutical Science, Dali University, Dali, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China
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Yi R, Bao W, Ao D, Bai YE, Wang L, Wuyun TN. Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species. Genes (Basel) 2023; 14:1959. [PMID: 37895308 PMCID: PMC10606377 DOI: 10.3390/genes14101959] [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: 09/14/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53-57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots.
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Affiliation(s)
- Ru Yi
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010018, China; (R.Y.); (W.B.); (D.A.); (Y.-e.B.)
| | - Wenquan Bao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010018, China; (R.Y.); (W.B.); (D.A.); (Y.-e.B.)
| | - Dun Ao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010018, China; (R.Y.); (W.B.); (D.A.); (Y.-e.B.)
| | - Yu-e Bai
- College of Forestry, Inner Mongolia Agricultural University, Hohhot 010018, China; (R.Y.); (W.B.); (D.A.); (Y.-e.B.)
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China;
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China
| | - Ta-na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China;
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China
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Zhou Q, Ni Y, Li J, Huang L, Li H, Chen H, Liu C. Multiple configurations of the plastid and mitochondrial genomes of Caragana spinosa. PLANTA 2023; 258:98. [PMID: 37831319 DOI: 10.1007/s00425-023-04245-6] [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: 06/14/2023] [Accepted: 09/15/2023] [Indexed: 10/14/2023]
Abstract
MAIN CONCLUSION In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes. Caragana spinosa belongs to the Papilionoidea subfamily and has significant pharmaceutical value. To explore the possible interaction between the organelle genomes, we assembled and analyzed the plastome and mitogenome of C. spinosa using the Illumina and Nanopore DNA sequencing data. The plastome of C. spinosa was 129,995 bp belonging to the inverted repeat lacking clade (IRLC), which contained 77 protein-coding genes, 29 tRNA genes, and four rRNA genes. The mitogenome was 378,373 bp long and encoded 54 unique genes, including 33 protein-coding, three ribosomal RNA (rRNA), and 18 transfer RNA (tRNA) genes. In addition to the single circular conformation, alternative conformations mediated by one and four repetitive sequences in the plastome and mitogenome were identified and validated, respectively. The inverted repeat (PDR12, the 12th dispersed repeat sequence in C. spinosa plastome) of plastome mediating recombinant was conserved in the genus Caragana. Furthermore, we identified 14 homologous fragments by comparing the sequences of mitogenome and plastome, including eight complete tRNA genes. A phylogenetic analysis of protein-coding genes extracted from the plastid and mitochondrial genomes revealed congruent topologies. Analyses of sequence divergence found one intergenic region, trnN-GUU-ycf1, exhibiting a high degree of variation, which can be used to develop novel molecular markers to distinguish the nine Caragana species accurately. This plastome and mitogenome of C. spinosa could provide critical information for the molecular breeding of C. spinosa and be used as a reference genome for other species of Caragana. In this study, we assembled the complete plastome and mitogenome of Caragana spinosa and explored the multiple configurations of the organelle genomes.
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Affiliation(s)
- Qingqing Zhou
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Jingling Li
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China
| | - Husheng Li
- Shenzhou Space Biotechnology Group, Beijing, 100190, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, No. 151, Malianwa North Road, Haidian District, Beijing, 100093, People's Republic of China.
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [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] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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Kim TH, Ha YH, Kim SC, Kim HJ. Characterization of the complete plastid genome and phylogenetic implication of Micranthes octopetala (Nakai) Y.I.Kim & Y.D.Kim (Saxifragaceae), endemic to Korea. Mitochondrial DNA B Resour 2023; 8:967-972. [PMID: 37711547 PMCID: PMC10498808 DOI: 10.1080/23802359.2023.2256051] [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: 06/07/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Micranthes octopetala (Nakai) Y.I.Kim & Y.D. Kim et al. 2015, which belongs to the family Saxifragaceae, is a perennial herb endemic to Korea. M. octopetala was originally treated as a synonym of M. manchuriensis. However, in 2015, molecular phylogenetic analysis confirmed that M. octopetala is an independent species. In this study, the plastid genome of M. octopetala was sequenced for the first time, and the taxonomic position of this species was identified. The complete plastid genome of M. octopetala has a total length of 149 751 bp (large single copy: 83 083 bp; small single copy: 17 196 bp; inverted repeat: 24 736 bp), containing 130 genes, including 79 CDS, 30 tRNAs, and 4 rRNAs. Moreover, the absence of intron in the rpl2 gene, which is a common feature of Saxifragaceae, was confirmed. Phylogenetic analysis based on 79 protein-coding genes from 21 species revealed that M. octopetala belongs to the genus Micranthes, being a sister to other Micranthes species. The plastid genome of M. octopetala obtained in this study provides fundamental information for future studies on the genus Micranthes.
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Affiliation(s)
- Tae-Hee Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-Si, Republic of Korea
| | - Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-Si, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-Si, Republic of Korea
| | - Hyuk-Jin Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon-Si, Republic of Korea
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Yue M, Chen H, Xuan L, Yang Y, Chong X, Li M, Yu C, Lu X, Zhang F. Novel molecular markers for Taxodium breeding from the chloroplast genomes of four artificial Taxodium hybrids. Front Genet 2023; 14:1193023. [PMID: 37600666 PMCID: PMC10433758 DOI: 10.3389/fgene.2023.1193023] [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: 03/24/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Taxodium "Zhongshanshan" are a group of intraspecific Taxodium hybrids with superparental dominance and high ecological and economic value in southern China. Identifying the parentage of hybrids, especially the male parent, is critically important for genetic studies. However, the large nuclear genomes of members of the genus Taxodium pose a major challenge for the development of molecular markers. Here, we developed novel molecular markers by conducting a comparative analysis of the chloroplast genomes of four artificial Taxodium hybrids and their parents. The lengths of the whole chloroplast genome ranged from 131,942 to 132,128 bp, and the total guanine (GC) content of the chloroplast genomes ranged from 34.6% to 35.81%. A total of 120 unique genes were identified, including 83 protein-coding genes, 33 transfer RNAs, and four ribosomal RNAs. There were 69-71 simple sequence repeats were detected in the four hybrids. Phylogenetic analysis revealed that these hybrids clustered with their paternal parents. Similar findings were obtained by analysis of the GC content of protein-coding genes. Molecular markers were developed using the highly variable regions of the chloroplast genomes, and polymerase chain reaction (PCR) assays revealed that these markers were effective for identifying the male parents of these hybrids. Our findings indicate for the first time that the chloroplast genomes of Taxodium are paternally inherited. Generally, these molecular markers could facilitate breeding and genetic studies of Taxodium.
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Affiliation(s)
- Minghua Yue
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Lei Xuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Ying Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xinran Chong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Mingzhi Li
- Guangzhou Bio&Data Technology Co., Ltd., Guangzhou, China
| | - ChaoGuang Yu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaoqing Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Fan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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Ibrahim AA, Alwutayd KM, Safhi FA, Alshegaihi RM, Alqurashi M, Alyamani A, Aloufi S, Alharthi B, Fayad E, Abd El-Moneim D. Characterization and comparative genomic analyses of complete chloroplast genome on Trema orientalis L. GENETIC RESOURCES AND CROP EVOLUTION 2023. [DOI: 10.1007/s10722-023-01678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 09/02/2023]
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Xia Q, Zhang H, Lv D, El-Kassaby YA, Li W. Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes. BMC Genomics 2023; 24:346. [PMID: 37349702 DOI: 10.1186/s12864-023-09439-6] [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: 08/02/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. RESULTS Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. CONCLUSION We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
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Affiliation(s)
- Qijing Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hongbin Zhang
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Dong Lv
- Gansu Province Academy of Qilian Water Resource Conservation Forests Research Institute, Zhangye, 734031, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Kim HB, Lee DG, Kim SC. Plastomes of Sonchus (Asteraceae) endemic to the Atlantic Madeira archipelago: Genome structure, comparative analysis, and phylogenetic relationships. PLoS One 2023; 18:e0287523. [PMID: 37347743 PMCID: PMC10286973 DOI: 10.1371/journal.pone.0287523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
The woody Sonchus alliance, a spectacular example of adaptive radiation with six genera and approximately 31 species, is found exclusively on three Macaronesian Islands (Madeira, Canaries, and Cape Verdes) in the Atlantic Ocean. Four of the Sonchus taxa are restricted to Madeira, including shrubs and small trees at higher elevations (S. fruticosus and S. pinnatus), and caudex perennials in the lower coastal areas (S. ustulatus subsp. maderensis and S. ustulatus subsp. ustulatus). The Madeiran Sonchus stemmed from a single colonization event that originated from the Canaries < 3 million years ago. However, the plastome evolution and species relationships remains insufficiently explored. We therefore assembled and characterized the plastomes of four Sonchus taxa from Madeira and conducted a phylogenomic analysis. We found highly conserved plastome sequences among the taxa, further supporting a single and recent origin. We also found highly conserved plastomes among the cosmopolitan weedy Sonchus, Macaronesian Sonchus in the Atlantic, and Juan Fernández Islands Dendroseris in the Pacific. Furthermore, we identified four mutation hotspot regions (trnK-rps16, petN-psbM, ndhF-Ψycf1, and ycf1) and simple sequence repeat motifs. This study strongly supports the monophyly of Madeiran Sonchus. However, its relationship with the remaining woody Sonchus alliance from the Canary Islands requires further investigation.
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Affiliation(s)
- Hye-Been Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
- R&I Center, COSMAX BTI, Pangyo Inno Valley E255, Seongnam, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo Inno Valley E255, Seongnam, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
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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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Shi W, Hu S, Song W, Huang Y, Shi C, Wang S. Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus ( Rhamnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:855-869. [PMID: 37520808 PMCID: PMC10382440 DOI: 10.1007/s12298-023-01331-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01331-7.
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Affiliation(s)
- Wenbo Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Siqi Hu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Yahui Huang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204 China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042 China
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Xie YN, Qi QQ, Li WH, Li YL, Zhang Y, Wang HM, Zhang YF, Ye ZH, Guo DP, Qian Q, Zhang ZF, Yan N. Domestication, breeding, omics research, and important genes of Zizania latifolia and Zizania palustris. FRONTIERS IN PLANT SCIENCE 2023; 14:1183739. [PMID: 37324716 PMCID: PMC10266587 DOI: 10.3389/fpls.2023.1183739] [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: 03/10/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Wild rice (Zizania spp.), an aquatic grass belonging to the subfamily Gramineae, has a high economic value. Zizania provides food (such as grains and vegetables), a habitat for wild animals, and paper-making pulps, possesses certain medicinal values, and helps control water eutrophication. Zizania is an ideal resource for expanding and enriching a rice breeding gene bank to naturally preserve valuable characteristics lost during domestication. With the Z. latifolia and Z. palustris genomes completely sequenced, fundamental achievements have been made toward understanding the origin and domestication, as well as the genetic basis of important agronomic traits of this genus, substantially accelerating the domestication of this wild plant. The present review summarizes the research results on the edible history, economic value, domestication, breeding, omics research, and important genes of Z. latifolia and Z. palustris over the past decades. These findings broaden the collective understanding of Zizania domestication and breeding, furthering human domestication, improvement, and long-term sustainability of wild plant cultivation.
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Affiliation(s)
- Yan-Ning Xie
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qian-Qian Qi
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wan-Hong Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ya-Li Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yu Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Hui-Mei Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Fen Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Zi-Hong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - De-Ping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ning Yan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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Weng L, Jiang Y, Wang Y, Zhang X, Zhou P, Wu M, Li H, Sun H, Chen S. Chloroplast genome characteristics and phylogeny of the sinodielsia clade (apiaceae: apioideae). BMC PLANT BIOLOGY 2023; 23:284. [PMID: 37246219 DOI: 10.1186/s12870-023-04271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The Sinodielsia clade of the subfamily Apioideae (Apiacieae) was established in 2008, and it is composed of 37 species from 17 genera. Its circumscription is still poorly delimited and unstable, and interspecific relationships in the clade lack comprehensive analysis. Chloroplast (cp.) genomes provide valuable and informative data sources for evolutionary biology and have been widely used in studies on plant phylogeny. To infer the phylogenetic history of the Sinodielsia clade, we assembled complete cp. genomes of 39 species and then performed phylogenetic analysis based on these cp. genome sequence data combined with 66 published cp. genomes from 16 genera relative to the Sinodielsia clade. RESULTS These 39 newly assembled genomes had a typical quadripartite structure with two inverted repeat regions (IRs: 17,599-31,486 bp) separated by a large single-copy region (LSC: 82,048-94,046 bp) and a small single-copy region (SSC: 16,343-17,917 bp). The phylogenetic analysis showed that 19 species were clustered into the Sinodielsia clade, and they were divided into two subclades. Six mutation hotspot regions were detected from the whole cp. genomes among the Sinodielsia clade, namely, rbcL-accD, ycf4-cemA, petA-psbJ, ycf1-ndhF, ndhF-rpl32 and ycf1, and it was found that ndhF-rpl32 and ycf1 were highly variable in the 105 sampled cp. genomes. CONCLUSION The Sinodielsia clade was subdivided into two subclades relevant to geographical distributions, except for cultivated and introduced species. Six mutation hotspot regions, especially ndhF-rpl32 and ycf1, could be used as potential DNA markers in the identification and phylogenetic analyses of the Sinodielsia clade and Apioideae. Our study provided new insights into the phylogeny of the Sinodielsia clade and valuable information on cp. genome evolution in Apioideae.
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Affiliation(s)
- Long Weng
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yunhui Jiang
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Yong Wang
- Yunnan Institute of Forest Inventory and Planning, Kunming, 650051, China
| | - Xuemei Zhang
- Yunnan Key Laboratory of Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Ping Zhou
- College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Mei Wu
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Hongzhe Li
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shaotian Chen
- College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
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Ma D, Ding Q, Zhao Z, Han X, Zheng HL. Chloroplast genome analysis of three Acanthus species reveal the adaptation of mangrove to intertidal habitats. Gene 2023; 873:147479. [PMID: 37182557 DOI: 10.1016/j.gene.2023.147479] [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: 03/04/2023] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
Acanthus is a distinctive genus that covers three species with different ecological niches including Acanthus mollis (arid terrestrial), Acanthus leucostachyus (damp forest) and Acanthus ilicifolius (coastal intertidal). It is an intriguing question how these species evolved from terrestrial to coastal intertidal. In the present study, we assembled chloroplast genomes of A. ilicifolius, A. leucostachyus and A. mollis, which exhibited typical quadripartite structures. The sizes were 150,758, 154,686 and 150,339 bp that comprised a large single copy (LSC, 82,963, 86,461 and 82,612 bp), a small single copy (SSC, 17,191, 17,511 and 17,019 bp), and a pair of inverted repeats (IRs, 25,302, 25,357 and 25,354 bp), respectively. Gene annotation revealed that A. ilicifolius, A. leucostachyus and A. mollis contained 113, 112 and 108 unique genes, each of which contained 79, 79 and 74 protein-coding genes, 30, 29 and 30 tRNAs, and 4 rRNA genes, respectively. Differential gene analysis revealed plenty of ndhs gene deletions in the terrestrial plant A. mollis. Nucleotide diversity analysis showed that the psbK, ycf1, ndhG, and rpl22 have the highest nucleotide variability. Compared to A. leucostachyus and A. mollis, seven genes in A. ilicifolius underwent positive selection. Among them, the atpF gene showed a strong positive selection throughout terrestrial to marine evolution and was important for adaptation to coastal intertidal habitats. Phylogenetic analysis indicated that A. ilicifolius has a closer genetic relationship with A. leucostachyus than A. mollis which further confirmed the evolutionary direction of Acanthus going from terrestrial to coastal intertidal zones.
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Affiliation(s)
- Dongna Ma
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiansu Ding
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhizhu Zhao
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Han
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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Postel Z, Mauri T, Lensink MF, Touzet P. What is the potential impact of genetic divergence of plastid ribosomal genes between Silene nutans lineages in hybrids? An in silico approach using the 3D structure of the plastid ribosome. FRONTIERS IN PLANT SCIENCE 2023; 14:1167478. [PMID: 37223795 PMCID: PMC10201985 DOI: 10.3389/fpls.2023.1167478] [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: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/25/2023]
Abstract
Introduction Following the integration of cyanobacteria into the eukaryotic cells, many genes were transferred from the plastid to the nucleus. As a result, plastid complexes are encoded both by plastid and nuclear genes. Tight co-adaptation is required between these genes as plastid and nuclear genomes differ in several characteristics, such as mutation rate and inheritance patterns. Among these are complexes from the plastid ribosome, composed of two main subunits: a large and a small one, both composed of nuclear and plastid gene products. This complex has been identified as a potential candidate for sheltering plastid-nuclear incompatibilities in a Caryophyllaceae species, Silene nutans. This species is composed of four genetically differentiated lineages, which exhibit hybrid breakdown when interlineage crosses are conducted. As this complex is composed of numerous interacting plastid-nuclear gene pairs, in the present study, the goal was to reduce the number of gene pairs that could induce such incompatibilities. Method We used the previously published 3D structure of the spinach ribosome to further elucidate which of the potential gene pairs might disrupt plastid-nuclear interactions within this complex. After modeling the impact of the identified mutations on the 3D structure, we further focused on one strongly mutated plastid-nuclear gene pair: rps11-rps21. We used the centrality measure of the mutated residues to further understand if the modified interactions and associated modified centralities might be correlated with hybrid breakdown. Results and discussion This study highlights that lineage-specific mutations in essential plastid and nuclear genes might disrupt plastid-nuclear protein interactions of the plastid ribosome and that reproductive isolation correlates with changes in residue centrality values. Because of this, the plastid ribosome might be involved in hybrid breakdown in this system.
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Affiliation(s)
- Zoé Postel
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
| | - Théo Mauri
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Marc F. Lensink
- Univ. Lille, CNRS, UMR 8576 – UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France
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Ahmad W, Asaf S, Al-Rawahi A, Al-Harrasi A, Khan AL. Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae). Sci Rep 2023; 13:7436. [PMID: 37156827 PMCID: PMC10167353 DOI: 10.1038/s41598-023-34477-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/02/2023] [Indexed: 05/10/2023] Open
Abstract
The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.
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Affiliation(s)
- Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, Nizwa, 616, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA.
- Department of Biology and Biochemistry, University of Houston, Houston, USA.
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Lee C, Ruhlman TA, Jansen RK. Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades. Mol Phylogenet Evol 2023; 182:107760. [PMID: 36921696 DOI: 10.1016/j.ympev.2023.107760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.
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Affiliation(s)
- Chaehee Lee
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA.
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
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Youssef D, El-Bakatoushi R, Elframawy A, El-Sadek L, Badan GE. Molecular phylogenetic study of flavonoids in medicinal plants: a case study family Apiaceae. JOURNAL OF PLANT RESEARCH 2023; 136:305-322. [PMID: 36853579 PMCID: PMC10126080 DOI: 10.1007/s10265-023-01442-y] [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: 01/03/2023] [Accepted: 02/12/2023] [Indexed: 05/25/2023]
Abstract
The current study examined the phylogenetic pattern of medicinal species of the family Apiaceae based on flavonoid groups production, as well as the overall mechanism of the key genes involved in flavonol and flavone production. Thirteen species of the family Apiaceae were used, including Eryngium campestre from the subfamily Saniculoideae, as well as Cuminum cyminum, Carum carvi, Coriandrum sativum, Apium graveolens, Petroselinum crispum, Pimpinella anisum, Anethum graveolens, Foeniculum vulgare, Daucus carota, Ammi majus, Torilis arvensis, and Deverra tortuosa from the subfamily Apioideae. The seeds were cultivated, and the leaves were collected to estimate flavonoids and their groups, physiological factors, transcription levels of flavonol and flavone production-related genes. The phylogenetic relationship between the studied species was established using the L-ribosomal 16 (rpl16) chloroplast gene. The results revealed that the studied species were divided into two patterns: six plant species, E. campestre, C. carvi, C. sativum, P. anisum, An. graveolens, and D. carota, contained low content of flavonoids, while the other seven species had high content. This pattern of flavonoids production coincided with the phylogenetic relationships between the studied species. In contrast, the phylogeny of the flavonol and flavone synthase genes was incompatible with the quantitative production of their products. The study concluded that the increment in the production of flavonol depends on the high expression of chalcone synthase, chalcone isomerase, flavanone 3 hydroxylase, flavonol synthase, the increase of Abscisic acid, sucrose, and phenyl ammonia lyase, while flavone mainly depends on evolution and on the high expression of the flavone synthase gene.
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Affiliation(s)
- Dalia Youssef
- Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, EgyptAlexandria, El-Shatby, 21526, Egypt.
| | - Ranya El-Bakatoushi
- Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, EgyptAlexandria, El-Shatby, 21526, Egypt
| | - Asmaa Elframawy
- Nucleic Acids Research Department, Genetic Engineering & Biotechnology Research Institute (GEBRI), City for Scientific Research and Technological Applications, Borg El-Arab, Alexandria, 21933, Egypt
| | - Laila El-Sadek
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Camp Caesar, Alexandria, 21525, Egypt
| | - Ghada El Badan
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Camp Caesar, Alexandria, 21525, Egypt
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Alshegaihi RM, Mansour H, Alrobaish SA, Al Shaye NA, Abd El-Moneim D. The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis. Genes (Basel) 2023; 14:genes14050976. [PMID: 37239336 DOI: 10.3390/genes14050976] [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: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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50
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Tian R, Aou X, Song B, Li Z, He X, Zhou S. Plastid Phylogenomic Analyses Reveal a Cryptic Species of Ligusticopsis (Apiaceae, Angiosperms). Int J Mol Sci 2023; 24:ijms24087419. [PMID: 37108580 PMCID: PMC10138589 DOI: 10.3390/ijms24087419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Ligusticopsis litangensis is identified and described as a cryptic species from Sichuan Province, China. Although the distribution of this cryptic species overlaps with that of Ligusticopsis capillacea and Ligusticopsis dielsiana, the morphological boundaries between them are explicit and have obviously distinguishable characters. The main distinguishing features of the cryptic species are as follows: long conical multi-branched roots, very short pedicels in compound umbels, unequal rays, oblong-globose fruits, 1-2 vittae per furrow and 3-4 vittae on the commissure. The above-mentioned features differ somewhat from other species within the genus Ligusticopsis, but generally coincide with the morphological boundaries defined for the genus Ligusticopsis. To determine the taxonomic position of L. litangensis, we sequenced and assembled the plastomes of L. litangensis and compared them with the plastomes of 11 other species of the genus Ligusticopsis. Notably, both phylogenetic analyses based on ITS sequences and the complete chloroplast genome robustly supported that three accessions of L. litangensis are monophyletic clade and then nested in Ligusticopsis genus. Moreover, the plastid genomes of 12 Ligusticopsis species, including the new species, were highly conserved in terms of gene order, gene content, codon bias, IR boundaries and SSR content. Overall, the integration of morphological, comparative genomic and phylogenetic evidence indicates that Ligusticopsis litangensis actually represents a new species.
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Affiliation(s)
- Rongming Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xueyimu Aou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Boni Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zixuan Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xingjin He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Songdong Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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