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Zhang T, Li M, Zhu X, Li S, Guo M, Guo C, Shu Y. Comparative Chloroplast Genomes Analysis Provided Adaptive Evolution Insights in Medicago ruthenica. Int J Mol Sci 2024; 25:8689. [PMID: 39201375 PMCID: PMC11354556 DOI: 10.3390/ijms25168689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
A perennial leguminous forage, Medicago ruthenica has outstanding tolerance to abiotic stresses. The genome of Medicago ruthenica is large and has a complex genetic background, making it challenging to accurately determine genetic information. However, the chloroplast genome is widely used for researching issues related to evolution, genetic diversity, and other studies. To better understand its chloroplast characteristics and adaptive evolution, chloroplast genomes of 61 Medicago ruthenica were assembled (including 16 cultivated Medicago ruthenica germplasm and 45 wild Medicago ruthenica germplasm). These were used to construct the pan-chloroplast genome of Medicago ruthenica, and the chloroplast genomes of cultivated and wild Medicago ruthenica were compared and analyzed. Phylogenetic and haplotype analyses revealed two main clades of 61 Medicago ruthenica germplasm chloroplast genomes, distributed in eastern and western regions. Meanwhile, based on chloroplast variation information, 61 Medicago ruthenica germplasm can be divided into three genetic groups. Unlike the phylogenetic tree constructed from the chloroplast genome, a new intermediate group has been identified, mainly consisting of samples from the eastern region of Inner Mongolia, Shanxi Province, and Hebei Province. Transcriptomic analysis showed that 29 genes were upregulated and three genes were downregulated. The analysis of these genes mainly focuses on enhancing plant resilience and adapting adversity by stabilizing the photosystem structure and promoting protein synthesis. Additionally, in the analysis of adaptive evolution, the accD, clpP and ycf1 genes showed higher average Ka/Ks ratios and exhibited significant nucleotide diversity, indicating that these genes are strongly positively selected. The editing efficiency of the ycf1 and clpP genes significantly increases under abiotic stress, which may positively contribute to plant adaptation to the environment. In conclusion, the construction and comparative analysis of the complete chloroplast genomes of 61 Medicago ruthenica germplasm from different regions not only revealed new insights into the genetic variation and phylogenetic relationships of Medicago ruthenica germplasm, but also highlighted the importance of chloroplast transcriptome analysis in elucidating the model of chloroplast responses to abiotic stress. These provide valuable information for further research on the adaptive evolution of Medicago ruthenica.
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Affiliation(s)
| | | | | | | | | | | | - Yongjun Shu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (T.Z.); (M.L.); (X.Z.); (S.L.); (M.G.); (C.G.)
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Huang Y, Jin XJ, Zhang CY, Li P, Meng HH, Zhang YH. Plastome evolution of Engelhardia facilitates phylogeny of Juglandaceae. BMC PLANT BIOLOGY 2024; 24:634. [PMID: 38971744 PMCID: PMC11227234 DOI: 10.1186/s12870-024-05293-0] [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: 03/29/2024] [Accepted: 06/12/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. RESULTS The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn't support rapid radiation occurred in the evolution history of Engelhardia. CONCLUSION Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.
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Affiliation(s)
- Yue Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
| | - Xin-Jie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China
| | - Can-Yu Zhang
- Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Pan Li
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yong-Hua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
- Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
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Liu S, Veranso-Libalah MC, Sukhorukov AP, Sun X, Nilova MV, Kushunina M, Mamut J, Wen Z. Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence. BMC PLANT BIOLOGY 2024; 24:456. [PMID: 38789931 PMCID: PMC11127444 DOI: 10.1186/s12870-024-05164-8] [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: 11/06/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences. RESULTS We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat. CONCLUSIONS Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).
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Affiliation(s)
- Shuai Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Marie Claire Veranso-Libalah
- Biodiversität und Evolution der Pflanzen, Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 830052, München, Germany
| | - Alexander P Sukhorukov
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation.
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation.
| | - Xuegang Sun
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Maya V Nilova
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Maria Kushunina
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation
- Department of Plant Physiology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Jannathan Mamut
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhibin Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Urumqi, 830011, China.
- Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, Urumqi, 830011, China.
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Wu L, Fan P, Cai J, Zang C, Lin Y, Xu Z, Wu Z, Gao W, Song J, Yao H. Comparative genomics and phylogenomics of the genus Glycyrrhiza (Fabaceae) based on chloroplast genomes. Front Pharmacol 2024; 15:1371390. [PMID: 38515836 PMCID: PMC10955637 DOI: 10.3389/fphar.2024.1371390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Glycyrrhiza (Fabaceae) species are rich in metabolites and widely used in medicine. Research on the chloroplast genome of Glycyrrhiza is important for understanding its phylogenetics, biogeography, genetic diversity, species identification, and medicinal properties. In this study, comparative genomics and phylogenomics of Glycyrrhiza were analyzed based on the chloroplast genome. The chloroplast genomes of six Glycyrrhiza species were obtained using various assembly and annotation tools. The final assembled chloroplast genome sizes for the six Glycyrrhiza species ranged from 126,380 bp to 129,115 bp, with a total of 109-110 genes annotated. Comparative genomics results showed that the chloroplast genomes of Glycyrrhiza showed typically lacking inverted repeat regions, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. Bioinformatics analysis revealed the presence of 69-96 simple sequence repeats and 61-138 long repeats in the chloroplast genomes. Combining the results of mVISTA and nucleotide diversity, four highly variable regions were screened for species identification and relationship studies. Selection pressure analysis indicated overall purifying selection in the chloroplast genomes of Glycyrrhiza, with a few positively selected genes potentially linked to environmental adaptation. Phylogenetic analyses involving all tribes of Fabaceae with published chloroplast genomes elucidated the evolutionary relationships, and divergence time estimation estimated the chronological order of species differentiations within the Fabaceae family. The results of phylogenetic analysis indicated that species from the six subfamilies formed distinct clusters, consistent with the classification scheme of the six subfamilies. In addition, the inverted repeat-lacking clade in the subfamily Papilionoideae clustered together, and it was the last to differentiate. Co-linear analysis confirmed the conserved nature of Glycyrrhiza chloroplast genomes, and instances of gene rearrangements and inversions were observed in the subfamily Papilionoideae.
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Affiliation(s)
- Liwei Wu
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Panhui Fan
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaying Cai
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxi Zang
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yulin Lin
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhengjun Wu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen, China
| | - Wei Gao
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen, China
| | - Jingyuan Song
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Hui Yao
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
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Wei Z, Chen F, Ding H, Liu W, Yang B, Geng J, Chen S, Guo S. Comparative Analysis of Six Chloroplast Genomes in Chenopodium and Its Related Genera ( Amaranthaceae): New Insights into Phylogenetic Relationships and the Development of Species-Specific Molecular Markers. Genes (Basel) 2023; 14:2183. [PMID: 38137004 PMCID: PMC10743295 DOI: 10.3390/genes14122183] [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: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Species within the genus Chenopodium hold significant research interest due to their nutritional richness and salt tolerance. However, the morphological similarities among closely related species and a dearth of genomic resources have impeded their comprehensive study and utilization. In the present research, we conduct the sequencing and assembly of chloroplast (cp) genomes from six Chenopodium and related species, five of which were sequenced for the first time. These genomes ranged in length from 151,850 to 152,215 base pairs, showcased typical quadripartite structures, and encoded 85 protein-coding genes (PCGs), 1 pseudogene, 37 tRNA genes, and 8 rRNA genes. Compared with the previously published sequences of related species, these cp genomes are relatively conservative, but there are also some interspecific differences, such as inversion and IR region contraction. We discerned 929 simple sequence repeats (SSRs) and a series of highly variable regions across 16 related species, predominantly situated in the intergenic spacer (IGS) region and introns. The phylogenetic evaluations revealed that Chenopodium is more closely related to genera such as Atriplex, Beta, Dysphania, and Oxybase than to other members of the Amaranthaceae family. These lineages shared a common ancestor approximately 60.80 million years ago, after which they diverged into distinct genera. Based on InDels and SNPs between species, we designed 12 pairs of primers for species identification, and experiments confirmed that they could completely distinguish 10 related species.
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Affiliation(s)
- Zixiang Wei
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Fangjun Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Hongxia Ding
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Wenli Liu
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Bo Yang
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Jiahui Geng
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shihua Chen
- College of Life Sciences, Yantai University, Yantai 264005, China; (Z.W.); (F.C.); (H.D.); (W.L.); (B.Y.); (J.G.)
| | - Shanli Guo
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
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Feng L, Zhao G, An M, Wang C, Yin Y. Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species. BMC Genomics 2023; 24:739. [PMID: 38053028 DOI: 10.1186/s12864-023-09838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Prunus cistena is an excellent color leaf configuration tree for urban landscaping in the world, which has purplish red leaves, light pink flowers, plant shape and high ornamental value. Genomic resources for P. cistena are scarce, and a clear phylogenetic and evolutionary history for this species has yet to be elucidated. Here, we sequenced and analyzed the complete chloroplast genome of P. cistena and compared it with related species of the genus Prunus based on the chloroplast genome. RESULTS The complete chloroplast genome of P. cistena is a 157,935 bp long typical tetrad structure, with an overall GC content of 36.72% and higher GC content in the in the inverted repeats (IR) regions than in the large single-copy (LSC) and small single-copy (SSC) regions. It contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The ycf3 and clpP genes have two introns, with the longest intron in the trnK-UUU gene in the LSC region. Moreover, the genome has a total of 253SSRs, with the mononucleotide SSRs being the most abundant. The chloroplast sequences and gene arrangements of P. cistena are highly conserved, with the overall structure and gene order similar to other Prunus species. The atpE, ccsA, petA, rps8, and matK genes have undergone significant positive selection in Prunus species. P. cistena has a close evolutionary relationship with P. jamasakura. The coding and IR regions are more conserved than the noncoding regions, and the chloroplast DNA sequences are highly conserved throughout the genus Prunus. CONCLUSIONS The current genomic datasets provide valuable information for further species identification, evolution, and phylogenetic research of the genus Prunus.
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Affiliation(s)
- Lijuan Feng
- Shandong Institute of Pomology, Taian, 271000, Shandong, China
| | - Guopeng Zhao
- Yantai Testing Center for Food and Drug, Yantai, 264005, Shandong, China
| | - Mengmeng An
- Zibo Academy of Agricultural Sciences, Zibo, 255000, Shandong, China
| | - Chuanzeng Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
| | - Yanlei Yin
- Shandong Institute of Pomology, Taian, 271000, Shandong, China.
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Chi X, Chen R, Zhang F, Chen S. Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, codon usage bias, and phylogenetic relationships. Genome 2023; 66:281-294. [PMID: 37159948 DOI: 10.1139/gen-2023-0014] [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] [Indexed: 05/11/2023]
Abstract
The phylogeny of the species from Phrymaceae and Mazaceae has undergone many adjustments and changes in recent years. Moreover, there is little plastome information on the Phrymaceae. In this study, we compared the plastomes of six species from the Phrymaceae and 10 species from the Mazaceae. The gene order, contents, and orientation of the 16 plastomes were found to be highly similar. A total of 13 highly variable regions were identified among the 16 species. An accelerated rate of substitution was found in the protein-coding genes, particularly cemA and matK. The combination of effective number of codons, parity rule 2, and neutrality plots revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported {Mazaceae [(Phrymaceae + Wightiaceae) + (Paulowniaceae + Orobanchaceae)]} relationships in the Lamiales. Our findings can provide useful information to analyze the phylogeny and molecular evolution within the Phrymaceae and Mazaceae.
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Affiliation(s)
- Xiaofeng Chi
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Ronglian Chen
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Faqi Zhang
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Shilong Chen
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
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Yang L, Deng S, Zhu Y, Da Q. Comparative chloroplast genomics of 34 species in subtribe Swertiinae (Gentianaceae) with implications for its phylogeny. BMC PLANT BIOLOGY 2023; 23:164. [PMID: 36977991 PMCID: PMC10044379 DOI: 10.1186/s12870-023-04183-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Subtribe Swertiinae, a medicinally significant and highly speciose Subtribe of family Gentianaceae. Despite previous extensive studies based on both morphology and molecular data, intergeneric and infrageneric relationships within subtribe Swertiinae remain controversial. METHODS Here, we employed four newly generated Swertia chloroplast genomes with thirty other published genomes to elucidate their genomic characteristics. RESULTS The 34 chloroplast genomes were small and ranged in size from 149,036 to 154,365 bp, each comprising two inverted repeat regions (size range 25,069-26,126 bp) that separated large single-copy (80,432-84,153 bp) and small single-copy (17,887-18,47 bp) regions, and all the chloroplast genomes showed similar gene orders, contents, and structures. These chloroplast genomes contained 129-134 genes each, including 84-89 protein-coding genes, 37 tRNAs, and 8 rRNAs. The chloroplast genomes of subtribe Swertiinae appeared to have lost some genes, such as rpl33, rpl2 and ycf15 genes. Comparative analyses revealed that two mutation hotspot regions (accD-psaI and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification in subtribe Swertiinae. Positive selection analyses showed that two genes (ccsA and psbB) had high Ka/Ks ratios, indicating that chloroplast genes may have undergone positive selection in their evolutionary history. Phylogenetic analysis showed that the 34 subtribe Swertiinae species formed a monophyletic clade, with Veratrilla, Gentianopsis and Pterygocalyx located at the base of the phylogenetic tree. Some genera of this subtribe, however, were not monophyletic, including Swertia, Gentianopsis, Lomatogonium, Halenia, Veratrilla and Gentianopsis. In addition, our molecular phylogeny was consistent with taxonomic classification of subtribe Swertiinae in the Roate group and Tubular group. The results of molecular dating showed that the divergence between subtrib Gentianinae and subtrib Swertiinae was estimated to occur in 33.68 Ma. Roate group and Tubular group in subtribe Swertiinae approximately diverged in 25.17 Ma. CONCLUSION Overall, our study highlighted the taxonomic utility of chloroplast genomes in subtribe Swertiinae, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of subtribe Swertiinae species.
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Affiliation(s)
- Lucun Yang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, 81008, China.
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resource, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China.
| | - Shengxue Deng
- Qinghai Environmental Science Research and Design Institute Co. Ltd, Xining, 810007, China
| | - Yongqing Zhu
- Maqin County Forestry and Grassland Station, Maqin, 814000, China
| | - Qilin Da
- Bureau of Forestry in Hualong County, Hualong, 810900, China
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Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
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Cai H, Gu X, Li Y, Ren Y, Yan S, Yang M. Cold Resistance of Euonymus japonicus Beihaidao Leaves and Its Chloroplast Genome Structure and Comparison with Celastraceae Species. PLANTS 2022; 11:plants11192449. [PMID: 36235317 PMCID: PMC9573587 DOI: 10.3390/plants11192449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/08/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022]
Abstract
Euonymus japonicus Beihaidao is one of the most economically important ornamental species of the Euonymus genus. There are approximately 97 genera and 1194 species of plants worldwide in this family (Celastraceae). Using E. japonicus Beihaidao, we conducted a preliminary study of the cold resistance of this species, evaluated its performance during winter, assembled and annotated its chloroplast genome, and performed a series of analyses to investigate its gene structure GC content, sequence alignment, and nucleic acid diversity. Our objectives were to understand the evolutionary relationships of the genus and to identify positive selection genes that may be related to adaptations to environmental change. The results indicated that E. japonicus Beihaidao leaves have certain cold resistance and can maintain their viability during wintering. Moreover, the chloroplast genome of E. japonicus Beihaidao is a typical double-linked ring tetrad structure, which is similar to that of the other four Euonymus species, E. hamiltonianus, E. phellomanus, E. schensianus, and E. szechuanensis, in terms of gene structure, gene species, gene number, and GC content. Compared to other Celastraceae species, the variation in the chloroplast genome sequence was lower, and the gene structure was more stable. The phylogenetic relationships of 37 species inferred that members of the Euonymus genus do not form a clade and that E. japonicus Beihaidao is closely related to E. japonicus and E. fortunei. A total of 11 functional positive selected genes were identified, which may have played an important role in the process of Celastraceae species adapting to environmental changes. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Celastraceae species.
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Affiliation(s)
- Hongyu Cai
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Xiaozheng Gu
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yongtan Li
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Yachao Ren
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
| | - Shufang Yan
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang 050050, China
| | - Minsheng Yang
- Forest Department, College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding 071000, China
- Correspondence: ; Tel.: +86-0312-752-8715
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11
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Zhang ZR, Yang X, Li WY, Peng YQ, Gao J. Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions. FRONTIERS IN PLANT SCIENCE 2022; 13:965335. [PMID: 36186045 PMCID: PMC9521400 DOI: 10.3389/fpls.2022.965335] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.
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Affiliation(s)
- Zheng-Ren Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Wei-Ying Li
- Southwest Research Center for Landscape Architecture Engineering Technology, State Forestry and Grassland Administration, Southwest Forestry University, Kunming, China
| | - Yan-Qiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
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AL-Juhani WS, Alharbi SA, Al Aboud NM, Aljohani AY. Complete chloroplast genome of the desert date (Balanites aegyptiaca (L.) Del. comparative analysis, and phylogenetic relationships among the members of Zygophyllaceae. BMC Genomics 2022; 23:626. [PMID: 36045328 PMCID: PMC9434970 DOI: 10.1186/s12864-022-08850-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Balanites aegyptiaca (L.) Delile, commonly known as desert date, is a thorny evergreen tree belonging to the family Zygophyllaceae and subfamily Tribuloideae that is widespread in arid and semiarid regions. This plant is an important source of food and medicines and plays an important role in conservation strategies for restoring degraded desert ecosystems. RESULTS In the present study, we sequenced the complete plastome of B. aegyptiaca. The chloroplast genome was 155,800 bp, with a typical four-region structure: a large single copy (LSC) region of 86,562 bp, a small single copy (SSC) region of 18,102 bp, and inverted repeat regions (IRa and IRb) of 25,568 bp each. The GC content was 35.5%. The chloroplast genome of B. aegyptiaca contains 107 genes, 75 of which coding proteins, 28 coding tRNA, and 4 coding rRNA. We did not observe a large loss in plastid genes or a reduction in the genome size in B. aegyptiaca, as found previously in some species belonging to the family Zygophyllaceae. However, we noticed a divergence in the location of certain genes at the IR-LSC and IR-SSC boundaries and loss of ndh genes relative to other species. Furthermore, the phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic classification of B. aegyptiaca as belonging to the Zygophyllaceae family. The plastome of B. aegyptiaca was found to be rich in single sequence repeats (SSRs), with a total of 240 SSRs. CONCLUSIONS The genomic data available from this study could be useful for developing molecular markers to evaluate population structure, investigate genetic variation, and improve production programs for B. aegyptiaca. Furthermore, the current data will support future investigation of the evolution of the family Zygophyllaceae.
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Affiliation(s)
- Widad S. AL-Juhani
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, 24381 Saudi Arabia
| | - Samah A. Alharbi
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, 24381 Saudi Arabia
| | - Nora M. Al Aboud
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, 24381 Saudi Arabia
| | - Ashwaq Y. Aljohani
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah, 24381 Saudi Arabia
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13
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Gene Losses and Plastome Degradation in the Hemiparasitic Species Plicosepalus acaciae and Plicosepalus curviflorus: Comparative Analyses and Phylogenetic Relationships among Santalales Members. PLANTS 2022; 11:plants11141869. [PMID: 35890506 PMCID: PMC9317152 DOI: 10.3390/plants11141869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/18/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
The Plicosepalus genus includes hemiparasitic mistletoe and belongs to the Loranthaceae family, and it has several medicinal uses. In the present study, we sequenced the complete plastomes of two species, Plicosepalus acaciae and Plicosepalus curviflorus, and compared them with the plastomes of photosynthetic species (hemiparasites) and nonphotosynthetic species (holoparasites) in the order Santalales. The complete chloroplast genomes of P. acaciae and P. curviflorus are circular molecules with lengths of 120,181 bp and 121,086 bp, respectively, containing 106 and 108 genes and 63 protein-coding genes, including 25 tRNA and 4 rRNA genes for each species. We observed a reduction in the genome size of P. acaciae and P. curviflorus and the loss of certain genes, although this reduction was less than that in the hemiparasite and holoparasitic cp genomes of the Santalales order. Phylogenetic analysis supported the taxonomic state of P. acaciae and P. curviflorus as members of the family Loranthaceae and tribe Lorantheae; however, the taxonomic status of certain tribes of Loranthaceae must be reconsidered and the species that belong to it must be verified. Furthermore, available chloroplast genome data of parasitic plants could help to strengthen efforts in weed management and encourage biotechnology research to improve host resistance.
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Chen C, Miao Y, Luo D, Li J, Wang Z, Luo M, Zhao T, Liu D. Sequence Characteristics and Phylogenetic Analysis of the Artemisia argyi Chloroplast Genome. FRONTIERS IN PLANT SCIENCE 2022; 13:906725. [PMID: 35795352 PMCID: PMC9252292 DOI: 10.3389/fpls.2022.906725] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/06/2022] [Indexed: 06/03/2023]
Abstract
Artemisia argyi Levl. et Van is an important Asteraceae species with a high medicinal value. There are abundant A. argyi germplasm resources in Asia, especially in China, but the evolutionary relationships of these varieties and the systematic localization of A. argyi in the family Asteraceae are still unclear. In this study, the chloroplast (cp) genomes of 72 A. argyi varieties were systematically analyzed. The 72 varieties originated from 47 regions in China at different longitudes, latitudes and altitudes, and included both wild and cultivated varieties. The A. argyi cp genome was found to be ∼151 kb in size and to contain 114 genes, including 82 protein-coding, 28 tRNA, and 4 rRNA genes. The number of short sequence repeats (SSRs) in A. argyi cp genomes ranged from 35 to 42, and most of them were mononucleotide A/T repeats. A total of 196 polymorphic sites were detected in the cp genomes of the 72 varieties. Phylogenetic analysis demonstrated that the genetic relationship between A. argyi varieties had a weak relationship with their geographical distribution. Furthermore, inverted repeat (IR) boundaries of 10 Artemisia species were found to be significantly different. A sequence divergence analysis of Asteraceae cp genomes showed that the variable regions were mostly located in single-copy (SC) regions and that the coding regions were more conserved than the non-coding regions. A phylogenetic tree was constructed using 43 protein-coding genes common to 67 Asteraceae species. The resulting tree was consistent with the traditional classification system; Artemisia species were clustered into one group, and A. argyi was shown to be closely related to Artemisia lactiflora and Artemisia montana. In summary, this study systematically analyzed the cp genome characteristics of A. argyi and compared cp genomes of Asteraceae species. The results provide valuable information for the definitive identification of A. argyi varieties and for the understanding of the evolutionary relationships between Asteraceae species.
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Preclinical Rodent Models of Arthritis and Acute Inflammation Indicate Immunomodulatory and Anti-Inflammatory Properties of Juglans regia Extracts. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1695701. [PMID: 35422870 PMCID: PMC9005270 DOI: 10.1155/2022/1695701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022]
Abstract
Juglans regia has been used to treat inflammatory and arthritic disorders in traditional medicine. The present study aimed to investigate the antiarthritic and anti-inflammatory potential of ethanolic leaves extract of J. regia. Arthritis was induced in rodents with Freund’s complete adjuvant. J. regia treatment was started on 8th day of arthritis induction and sustained for 20 days. Acute inflammatory models were developed using carrageenan, histamine, serotonin, and dextran. Qualitative and GC-MS analyses were also performed. Arthritis was determined using an arthritis scoring index and histopathological examination of ankle joints. RT-PCR was performed to determine the expression of pro-inflammatory markers (TNF-α, NF-κB, IL-6, IL-1β, and COX-2) and anti-inflammatory IL-4. PGE2 levels were evaluated using an ELISA. Blood and biochemical parameters were also determined. Paw edema was measured using a digital plethysmometer. Treatment with extracts inhibited arthritic development and attenuated paw edema along with all histopathological parameters. The expression levels of pro-inflammatory cytokines and COX-2 were downregulated, while IL-4 was upregulated. PGE2 levels were also reduced in extract-treated groups. Blood and biochemical parameters were nearly normalized in the treatment groups. Both extracts significantly inhibited carrageenan, histamine, serotonin, and dextran-induced paw edema. Qualitative phytochemical screening and GC-MS analysis confirmed that extracts possessed potential medicinal compounds. In conclusion, ethanol and n-hexane extracts of J. regia leaves have immunomodulatory and anti-inflammatory effects that ameliorate experimentally induced arthritis and edema. The inhibition of autacoids may also be one of the mechanisms inducing the immunomodulatory effect.
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Odago WO, Waswa EN, Nanjala C, Mutinda ES, Wanga VO, Mkala EM, Oulo MA, Wang Y, Zhang CF, Hu GW, Wang QF. Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2022; 12. [DOI: https:/doi.org/10.3389/fpls.2021.814833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.
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Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.-Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single-copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single-copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132-133 genes, including 85-87 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37-43 long repeats and 175-178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
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Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - ShuiFei Chen
- Research Center for Nature Conservation and BiodiversityState Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi MountainsState Environmental Protection Key Laboratory on BiosafetyNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaCollege of Biology and the EnvironmentKey Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationNanjing Forestry UniversityNanjingChina
| | - Hui Ding
- Research Center for Nature Conservation and BiodiversityState Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi MountainsState Environmental Protection Key Laboratory on BiosafetyNanjing Institute of Environmental Sciences, Ministry of Ecology and EnvironmentNanjingChina
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18
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Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships. LIFE (BASEL, SWITZERLAND) 2022; 12:life12010092. [PMID: 35054485 PMCID: PMC8778281 DOI: 10.3390/life12010092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/26/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023]
Abstract
Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.
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Xi J, Lv S, Zhang W, Zhang J, Wang K, Guo H, Hu J, Yang Y, Wang J, Xia G, Fan G, Wang X, Xiao L. Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. FRONTIERS IN PLANT SCIENCE 2022; 13:990064. [PMID: 36407576 PMCID: PMC9667483 DOI: 10.3389/fpls.2022.990064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/21/2022] [Indexed: 05/03/2023]
Abstract
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
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Affiliation(s)
- Jianwei Xi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Saibin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jingbo Zhang
- Department of Biological Sciences, St. John’s University - Queens, NY, United States
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Haobing Guo
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Jie Hu
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guangyi Fan
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Xinwang Wang
- Pecan Breeding and Genetics, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, United States
| | - Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
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Complete Chloroplast Genome Sequence of Sonchus brachyotus Helps to Elucidate Evolutionary Relationships with Related Species of Asteraceae. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9410496. [PMID: 34901281 PMCID: PMC8654571 DOI: 10.1155/2021/9410496] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022]
Abstract
Sonchus brachyotus DC. possesses both edible and medicinal properties and is widely distributed throughout China. In this study, the complete cp genome of S. brachyotus was sequenced and assembled. The total length of the complete S. brachyotus cp genome was 151,977 bp, including an LSC region of 84,553 bp, SSC region of 18,138 bp, and IR region of 24,643 bp. Sequence analyses revealed that the cp genome encoded 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content was 37.6%. One hundred mononucleotide microsatellites, 4 dinucleotide microsatellites, 67 trinucleotide microsatellites, 4 tetranucleotide microsatellites, and 1 long repeat were identified. The SSR frequency of the LSC region was significantly greater than that of the IR and SSC regions. In total, 175 SSRs and highly variable regions were recognized as potential cp markers. By analyzing the IR/LSC and IR/SSC boundaries, structural differences between S. brachyotus and 6 other species were detected. According to phylogenetic analyses, S. brachyotus was most closely related to S. arvensis and S. oleraceus. Overall, this study provides complete cp genome resources for S. brachyotus that will be beneficial for identifying potential molecular markers and evolutionary patterns of S. brachyotus and its closely related species.
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Complete Chloroplast Genomes of Three Salix Species: Genome Structures and Phylogenetic Analysis. FORESTS 2021. [DOI: 10.3390/f12121681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
High genetic diversity and low differentiation present challenges in taxonomy and systematics of Salix. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. Salix spathulifolia Seemen, S. cupularis Rehder, and S. annulifera C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of Salix was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows’ cp genomes revealed high similarity. Phylogenetic analysis indicated that S. spathulifolia was a basal taxon of clade I, while S. annulifera formed a monophyletic group with S. rorida Laksch.; S. cupularis was sister to S. suchowensis W.C. Cheng and S. psammophila Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae.
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Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021; 21:191. [PMID: 34674641 PMCID: PMC8529855 DOI: 10.1186/s12862-021-01917-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. RESULTS We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. CONCLUSIONS A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).
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Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021. [PMID: 34674641 DOI: 10.21203/rs.3.rs-495294/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. RESULTS We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. CONCLUSIONS A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).
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Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhang L, Wang S, Su C, Harris AJ, Zhao L, Su N, Wang JR, Duan L, Chang ZY. Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China. FRONTIERS IN PLANT SCIENCE 2021; 12:723622. [PMID: 34630471 PMCID: PMC8500179 DOI: 10.3389/fpls.2021.723622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 05/25/2023]
Abstract
The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245-80,439 bp), a small single-copy (SSC) region (16,285-17,146 bp), and a pair of inverted repeat (IR) regions (3,792-4,466 bp). These cp genomes contained 111-112 genes each, including 74-75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.
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Affiliation(s)
- Ling Zhang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
- College of Life Science, Tarim University, Alar, China
- Key Laboratory of Biological Resource Protection and Utilization of Tarim Basin Xinjiang Production & Construction Group, Alar, China
| | - Shu Wang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Chun Su
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - AJ Harris
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Liang Zhao
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Na Su
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Jun-Ru Wang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Lei Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhao-Yang Chang
- College of Life Science, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
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Sun J, Wang Y, Garran TA, Qiao P, Wang M, Yuan Q, Guo L, Huang L. Heterogeneous Genetic Diversity Estimation of a Promising Domestication Medicinal Motherwort Leonurus Cardiaca Based on Chloroplast Genome Resources. Front Genet 2021; 12:721022. [PMID: 34603384 PMCID: PMC8479170 DOI: 10.3389/fgene.2021.721022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/01/2021] [Indexed: 11/30/2022] Open
Abstract
Leonurus cardiaca has a long history of use in western herbal medicine and is applied for the treatment of gynaecological conditions, anxiety, and heart diseases. Because of its botanical relationship to the primary Chinese species, L. japonicus, and extensive medical indications that go beyond the traditional indications for the Chinese species, it is a promising medicinal resource. Therefore, the features of genetic diversity and variability in the species have been prioritized. To explore these issues, we sequenced the chloroplast genomes of 22 accessions of L. cardiaca from different geographical locations worldwide using high-throughput sequencing. The results indicate that L. cardiaca has a typical quadripartite structure and range from 1,51,236 bp to 1,51,831 bp in size, forming eight haplotypes. The genomes all contain 114 distinct genes, including 80 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Comparative analysis showed abundant diversity of single nucleotide polymorphisms (SNPs), indels, simple sequence repeats (SSRs) in 22 accessions. Codon usage showed highly similar results for L. cardiaca species. The phylogenetic and network analysis indicated 22 accessions forming four clades that were partly related to the geographical distribution. In summary, our study highlights the advantage of chloroplast genome with large data sets in intraspecific diversity evaluation and provides a new tool to facilitate medicinal plant conservation and domestication.
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Affiliation(s)
- Jiahui Sun
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yiheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Thomas Avery Garran
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Qiao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Academician workstation, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Mengli Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qingjun Yuan
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Comparative and phylogenetic analyses of the chloroplast genomes of species of Paeoniaceae. Sci Rep 2021; 11:14643. [PMID: 34282194 PMCID: PMC8289817 DOI: 10.1038/s41598-021-94137-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia.
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Chang H, Zhang L, Xie H, Liu J, Xi Z, Xu X. The Conservation of Chloroplast Genome Structure and Improved Resolution of Infrafamilial Relationships of Crassulaceae. FRONTIERS IN PLANT SCIENCE 2021; 12:631884. [PMID: 34276716 PMCID: PMC8281817 DOI: 10.3389/fpls.2021.631884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/10/2021] [Indexed: 06/04/2023]
Abstract
Crassulaceae are the largest family in the angiosperm order Saxifragales. Species of this family are characterized by succulent leaves and a unique photosynthetic pathway known as Crassulacean acid metabolism (CAM). Although the inter- and intrageneric relationships have been extensively studied over the last few decades, the infrafamilial relationships of Crassulaceae remain partially obscured. Here, we report nine newly sequenced chloroplast genomes, which comprise several key lineages of Crassulaceae. Our comparative analyses and positive selection analyses of Crassulaceae species indicate that the overall gene organization and function of the chloroplast genome are highly conserved across the family. No positively selected gene was statistically supported in Crassulaceae lineage using likelihood ratio test (LRT) based on branch-site models. Among the three subfamilies of Crassulaceae, our phylogenetic analyses of chloroplast protein-coding genes support Crassuloideae as sister to Kalanchoideae plus Sempervivoideae. Furthermore, within Sempervivoideae, our analyses unambiguously resolved five clades that are successively sister lineages, i.e., Telephium clade, Sempervivum clade, Aeonium clade, Leucosedum clade, and Acre clade. Overall, this study enhances our understanding of the infrafamilial relationships and the conservation of chloroplast genomes within Crassulaceae.
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Affiliation(s)
- Hong Chang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huanhuan Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystems, College of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea). FORESTS 2021. [DOI: 10.3390/f12070861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.
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Wu L, Cui Y, Wang Q, Xu Z, Wang Y, Lin Y, Song J, Yao H. Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes. PLANTA 2021; 254:14. [PMID: 34180013 DOI: 10.1007/s00425-021-03667-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
The chloroplast genomes of the five Crataegus species were shown to have a conserved genome structure. Complete chloroplast genome sequences were more suitable than highly variable regions for the identification and phylogenetic analysis of Crataegus species. Hawthorn, which is commonly used as a traditional Chinese medicine, is one of the most popular sour fruits and has high economic value. Crataegus pinnatifida var. pinnatifida and C. pinnatifida var. major are frequently adulterated with other Crataegus species on the herbal medicine market. However, most Crataegus plants are difficult to identify using traditional morphological methods. Here, we compared five Crataegus chloroplast (CP) genomes comprising two newly sequenced (i.e., C. pinnatifida var. pinnatifida and C. pinnatifida var. major) and three previously published CP genomes. The CP genomes of the five Crataegus species had a conserved genome structure, gene content and codon usage. The total length of the CP genomes was 159,654-159,865 bp. A total of 129-130 genes, including 84-85 protein-coding genes, 37 tRNA genes and 8 rRNA genes, were annotated. Bioinformatics analysis revealed 96-103 simple sequence repeats (SSRs) and 48-70 long repeats in the five CP genomes. Combining the results of mVISTA and nucleotide diversity, five highly variable regions were screened for species identification and relationship studies. Maximum likelihood trees were constructed on the basis of complete CP genome sequences and highly variable regions. The results showed that the former had higher discriminatory power for Crataegus species, indicating that the complete CP genome could be used as a super-barcode to accurately authenticate the five Crataegus species.
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Affiliation(s)
- Liwei Wu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yingxian Cui
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Qing Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Zhichao Xu
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Yu Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Yulin Lin
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Jingyuan Song
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China
| | - Hui Yao
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.
- Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, 100193, China.
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Wen F, Wu X, Li T, Jia M, Liu X, Liao L. The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China. BMC Genomics 2021; 22:161. [PMID: 33676415 PMCID: PMC7937279 DOI: 10.1186/s12864-021-07484-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily. RESULTS A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages. CONCLUSIONS This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
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Affiliation(s)
- Feng Wen
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Xiaozhu Wu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tongjian Li
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Mingliang Jia
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Xinsheng Liu
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Liang Liao
- School of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
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31
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Odago WO, Waswa EN, Nanjala C, Mutinda ES, Wanga VO, Mkala EM, Oulo MA, Wang Y, Zhang CF, Hu GW, Wang QF. Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships. FRONTIERS IN PLANT SCIENCE 2021; 12:814833. [PMID: 35211136 PMCID: PMC8862764 DOI: 10.3389/fpls.2021.814833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 05/12/2023]
Abstract
Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.
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Affiliation(s)
- Wyclif Ochieng Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Millicent Akinyi Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cai-Fei Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Cai-Fei Zhang,
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Guang-Wan Hu,
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Teske D, Peters A, Möllers A, Fischer M. Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14323-14333. [PMID: 32917087 DOI: 10.1021/acs.jafc.0c03001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.
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Affiliation(s)
- Doreen Teske
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alina Peters
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alexander Möllers
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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33
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Wu L, Nie L, Xu Z, Li P, Wang Y, He C, Song J, Yao H. Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of Three Paeonia Section Moutan Species (Paeoniaceae). Front Genet 2020; 11:980. [PMID: 33193580 PMCID: PMC7533573 DOI: 10.3389/fgene.2020.00980] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023] Open
Abstract
Analysis of the relationships among wild species of section Moutan in the plant genus Paeonia has traditionally been problematic. Interspecies relationships cannot be effectively determined using phenotypic traits alone or through analysis of nuclear or chloroplast DNA fragments. Elucidation of complete chloroplast genome sequences will aid the identification and phylogeny of these species. In this study, the complete chloroplast genomes of three sect. Moutan plants were sequenced and analyzed. Comparative and phylogenetic analyses of the complete chloroplast genomes of all eight species of sect. Moutan were then conducted. The three complete chloroplast genomes gained in this study showed four-part annular structures, and the genome length, structure, GC content, codon usage, and gene distribution were highly similar. There was greater variation in the noncoding regions of the sequences than in the conserved protein-coding regions. Sequence variations in the small single copy (SSC) regions and large single copy (LSC) regions were considerably greater than those in the inverted repeat (IR) regions. Phylogenetic analysis revealed that the species of sect. Moutan clustered in one branch and then subdivided into smaller branches. As for the three complete chloroplast genome sequences obtained in this study, Paeonia jishanensis clustered with another P. jishanensis sequence from the GenBank database, Paeonia qiui clustered with Paeonia rockii, and Paeonia delavayi var. lutea clustered with Paeonia ludlowii. It was also found that the complete chloroplast genomes, LSC regions, and SSC regions all showed great abilities in identification and phylogenetic analysis of the species of sect. Moutan, while IRs regions and highly variable regions were not suitable for the species of sect. Moutan.
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Affiliation(s)
- Liwei Wu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Liping Nie
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Zhichao Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Pei Li
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Chunnian He
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
| | - Hui Yao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Engineering Research Center of Chinese Medicine Resources, Ministry of Education, Beijing, China
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Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8542797. [PMID: 32626767 PMCID: PMC7306069 DOI: 10.1155/2020/8542797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 05/22/2020] [Indexed: 11/20/2022]
Abstract
The section Pallasia is one of the components of the genus Allium subgenus Allium (Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect. Pallasia species were reported, and a comparative analysis was performed with other three related Allium species. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (except Allium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary, A. pallasii exhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eight Allium species cluster into a group, and A. pallasii exhibit a close relationship with A. obliquum. Higher pairwise Ka/Ks ratios were found in A. schoenoprasoides compared to A. caeruleum and A. macrostemon while a lower value of Ka/Ks ratios was detected between A. caeruleum and A. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research in Allium.
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35
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Song XB, Ma QG, Zhou Y, Chang YY, Zhang JP, Pei D. The complete chloroplast genome of paradox ( Juglans major × J. regia), an interspecific hybrid in China. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2087-2088. [PMID: 33457753 PMCID: PMC7782917 DOI: 10.1080/23802359.2020.1765212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Paradox is one of the most important rootstock resources in USA and China walnut industry. In this study, we characterized the complete chloroplast genome of Paradox (Juglans major × J. regia) based on next generation sequencing. The circular complete chloroplast genome was 160,324 bp in length, containing a large single-copy (LSC) region of 89,852 bp, and a small single-copy (SSC) region of 18,410 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb) of 26,031 bp each. A total of 131 functional genes were encoded, consisted of 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 36.1% and the GC contents of the LSC, SSC, and IR regions were 33.7, 29.9, and 42.6%, respectively. The phylogenetic analysis by Neighbor-Joining showed that Paradox was relatively closely related to J. major compared to other species of Juglans genus. This complete chloroplast genome will provide valuable insight into evolution, molecular breeding, and phylogenetic analysis of Juglans species.
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Affiliation(s)
- Xiao-Bo Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qing-Guo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ye Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ying-Ying Chang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jun-Pei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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36
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Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. Int J Mol Sci 2020; 21:ijms21093280. [PMID: 32384622 PMCID: PMC7247323 DOI: 10.3390/ijms21093280] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/14/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.
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Xiong Y, Xiong Y, He J, Yu Q, Zhao J, Lei X, Dong Z, Yang J, Peng Y, Zhang X, Ma X. The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E478. [PMID: 32283660 PMCID: PMC7238141 DOI: 10.3390/plants9040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 01/31/2023]
Abstract
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.
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Affiliation(s)
- Yanli Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yi Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jun He
- State Key Laboratory of Exploration and Utilization of Crop Gene Resources in 10 Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in 11 Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan 12 Agricultural University, Chengdu 600031, China;
| | - Qingqing Yu
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Junming Zhao
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiong Lei
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Zhixiao Dong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jian Yang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yan Peng
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xinquan Zhang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiao Ma
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
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Ma QG, Huang Y, Song XB, Chang YY, Pei D. The complete chloroplast genome of Juglans cathayensis var. formosana (Hayata), an endemic in China. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1750984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Qing-guo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yong Huang
- Fujian Academy of Forestry Sciences, Fuzhou, China
| | - Xiao-bo Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ying-ying Chang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Ebrahimi A, Lawson SS, McKenna JR, Jacobs DF. Morpho-Physiological and Genomic Evaluation of Juglans Species Reveals Regional Maladaptation to Cold Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:229. [PMID: 32210997 PMCID: PMC7077431 DOI: 10.3389/fpls.2020.00229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/14/2020] [Indexed: 05/02/2023]
Abstract
Climate change may have unpredictable effects on the cold hardiness of woody species planted outside of their range of origin. Extreme undulations in temperatures may exacerbate susceptibility to cold stress, thereby interfering with productivity and ecosystem functioning. Juglans L. and their naturally occurring interspecific F1 hybrids, are distributed natively across many temperate regions, and J. regia has been extensively introduced. Cold hardiness, an environmental and genetic factor yet to be evaluated in many native and introduced Juglans species, may be a limiting factor under future climate change and following species introductions. We evaluated cold hardiness of native North American and Eastern Asian Juglans along with J. regia genotypes using field data from the Midwestern United States (Indiana), controlled freezing tests, and genome sequencing with close assessment of Juglans cold hardy genes. Many Juglans species previously screened for cold-hardiness were genotypes derived from the Midwest, California, and Europe. In 2014, despite general climate adaptation, Midwestern winter temperatures of -30°C killed J. regia originating from California; however, naturalized Midwestern J. regia survived and displayed low damage. Hybridization of J. regia with black walnut (J. nigra) and butternut (J. cinerea) produced F1s displaying greater cold tolerance than pure J. regia. Cold hardiness and growth are variable in Midwestern J. regia compared to native Juglans, East Asian Juglans, and F1 hybrids. Phylogeny analyses revealed that J. cinerea sorted with East Asian species using the nuclear genome but with North American species using the organellar genome. Investigation of selected cold hardy genes revealed that J. regia was distinct from other species and exhibited less genetic diversity than native Juglans species Average whole genome heterozygosity and Tajima's D for cold hardy genes was low within J. regia samples and significantly higher for hybrid as well as J. nigra. We confirmed that molecular and morpho-physiological data were highly correlated and thus can be used effectively to characterize cold hardiness in Juglans species. We conclude that the genetic diversity within local J. regia populations is low and additional germplasm is needed for development of more regionally adapted J. regia varieties.
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Affiliation(s)
- Aziz Ebrahimi
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States
| | - Shaneka S. Lawson
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, West Lafayette, IN, United States
| | - James R. McKenna
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, West Lafayette, IN, United States
| | - Douglass F. Jacobs
- Hardwood Tree Improvement and Regeneration Center, Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States
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Li H, Xie DF, Chen JP, Zhou SD, He XJ. Chloroplast genomic comparison of two sister species Allium macranthum and A. fasciculatum provides valuable insights into adaptive evolution. Genes Genomics 2020; 42:507-517. [PMID: 32146713 DOI: 10.1007/s13258-020-00920-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 02/14/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Allium macranthum and Allium fasciculatum are two sister species and their natural populations are separated by high mountains and deep valleys with exact opposite habitat. The chloroplast genome in angiosperms has showed useful for investigating plant evolution and systematic studies. OBJECTIVE Comparative analysis of these genomes revealed potential markers and phylogenetic analysis, and discuss the influence of positive selected sites on adaptive evolution. METHODS Here, we sequenced the complete chloroplast genomes of these two species and analyzed the repeat sequences components, nucleotide diversity, selection pressure and the phylogeny relationships with related species. RESULTS A typical quadripartite structure was detected with a genome size changed from 152,148 to 152,931 bp. We identified 67 and 79 simple sequence repeats in A. macranthum and A. fasciculatum, in which the mono-nucleotide repeats A/T possess the highest percentage. Three mutational hotspots (rpl32, rps16 and matK) at the SSC and LSC regions were observed, which showed remarkably higher Pi value (> 0.03). Additionally, eight genes (rpoA, atpF, cemA, rps4, ccsA, rpoC2, rpl14 and clpP) exhibited elevated pairwise Ka/Ks ratios in alpine species. Phylogenetic analyses based on the CDS sequences and the whole complete genomes showed same topologies with high support, and A. macranthum was closely clustered with A. fasciculatum within the fourteen Amaryllidaceae species. CONCLUSION Their coding proteins of these genes often functioned in chloroplast protein synthesis, gene transcription, energy transformation and regulation and photosynthesis. These results provide valuable insights into the alpine species adaptation and evolution.
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Affiliation(s)
- Hao Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, China.
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Luo X, Chen J. Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships with Juglans regia and J. sigillata by FISH, Early-Fruiting Gene Analysis, and SSR Analysis. FRONTIERS IN PLANT SCIENCE 2020; 11:27. [PMID: 32161605 PMCID: PMC7052499 DOI: 10.3389/fpls.2020.00027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 06/02/2023]
Abstract
Walnuts are economically important tree species in Sichuan Province (China) that provide heathy nuts. Fluorescence in situ hybridization (FISH) and analyses of an early-fruiting gene fragment and simple sequence repeats (SSRs) were used to distinguish Sichuan walnut cultivars and examine their relationships with Juglans regia L. and Juglans sigillata Dode. Thirty-four small chromosomes were counted in four Sichuan walnut cultivars. In the four cultivars, 5S rDNA was located in the proximal regions of two chromosomes (5 and 6), while (AG3T3)3 was located at both ends of each chromosome. The existence of the signal at both chromosome ends ensured accurate chromosome counts. 5S rDNA and (AG3T3)3 were not effective in identifying Sichuan walnut cultivars. Evolutionary analysis involving 32 early-fruiting nucleotide sequences from Sichuan walnut materials were performed with the maximum likelihood method. There were a total of 602 positions. All positions with gaps and missing data were eliminated, resulting in a final dataset of 562 positions. The ML tree with the highest log likelihood (-1607.82) revealed two obvious groups: one including materials of J. regia, which fruits 1 year after grafting, and another including materials of J. sigillata, which fruits >3 years after grafting. The early-fruiting gene fragment divided 22 walnut materials (10 walnut cultivars and 12 walnut accessions) into two groups, indicating that it was somewhat effective for distinguishing Sichuan walnut cultivars. Furthermore, 22 SSR loci were revealed to identify nine walnut cultivars. Eight cultivars were exclusively discerned by one SSR locus each: Chuanzao 1 [CUJRB307 (116) or CUJRA206a (182)], Chuanzao 2 [JSI-73 (154)], Shuangzao [CUJRB103a (123), CUJRB218 (144), JSI-71 (146), or CUJRA206a (176)], Shimianju [ZMZ11 (138)], Meigupao [CUJRB218 (149), CUJRB103a (151), or CUJRA206a (190)], Muzhilinhe [CUJRB220 (136), ZMZ11 (147), CUJRC310 (156), or JSI-73 (166)], Maerkang [CUJRA124 (154), CUJRB218 (159), or CUJRA123 (182)], Yanyuanzao [CUJRA124 (150) or CUJRA206a (192)]. The Shuling cultivar was identified by the combination of ZMZ11 (148) and other SSR loci, which distinguished and excluded the Chuanzao 1 and Yanyuanzao cultivars. Our results will guide the identification and breeding of Sichuan walnut cultivars.
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Zhang RS, Yang J, Hu HL, Xia RX, Li YP, Su JF, Li Q, Liu YQ, Qin L. A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima. Int J Biol Macromol 2020; 152:340-348. [PMID: 32109476 DOI: 10.1016/j.ijbiomac.2020.02.201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/18/2022]
Abstract
The Sawtooth Oak, Quercus acutissima Carruth., is an economically and ecologically important tree species in the family Fagaceae with a wide distribution in China. Here, we examined its intraspecific chloroplast (cp) genome variability using available and a newly sequenced genome. The new cp genome comes from a Q. acutissima individual collected from Shenyang (Northeast China; "Q. acutissima Shenyang" in the following), and then is compared with two recently published cp genomes from Tongchuan (Northwest China) and Nanjing (East China). The cp genome of Q. acutissima Shenyang exhibits a slightly larger genome size than the other two individuals, although each encodes 86 protein-coding genes, 40 tRNA genes and eight rRNA genes. We also found the length difference for the IR/SC boundary region among the three cp genomes. Sequence comparison revealed a high intraspecific genetic divergence: the three cp genomes differ by 332 sequence patterns including 77 single nucleotide polymorphisms, and 255 indels (each gap considered) scattering across 67 regions. Phylogenetic analyses based on the cp genome recovered the split between the subgenus Cerris and the subgenus Quercus, but revealed that three Q. acutissima individuals did not cluster together, indicating that even complete cp genome data fail to reproduce species boundaries in Asian members of section Cerris. Our results show that more complete plastomes covering remote ranges needs to be sequenced to provide a solid backbone for future population-scale in-depth studies and phylogenetic analysis of section Cerris.
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Affiliation(s)
- Ru-Song Zhang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jian Yang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Hua-Lei Hu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Run-Xi Xia
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yu-Ping Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jun-Fang Su
- Center for Experimental Teaching, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qun Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Yan-Qun Liu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Li Qin
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
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The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis. FORESTS 2020. [DOI: 10.3390/f11020207] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Research Highlights: For the first time, the complete chloroplast (cp) genome of Carya illinoinensis cv. ‘Pawnee’ was de novo assembled. Comprehensive analysis the cp genome of C. illinoinensis revealed potential cpDNA markers for intraspecies identification, genes involved in adaptation, and its phylogenetic position. Background and Objectives: C. illinoinensis is an economically important nut tree in the family Juglandaceae. Cp-derived markers are helpful for genetic research, but they still need to be developed in C. illinoinensis. Additionally, the adaptation and phylogenetic relationships of C. illinoinensis have not been revealed based on the complete cp genome. Materials and Methods: Chloroplast genomic DNA of C. illinoinensis cv. ‘Pawnee’ was extracted and subjected to Illumina sequencing. Results: The cp genome is 160,819 bp in size, exhibiting a typical quadripartite structure with a large single copy (LSC) of 90,022 bp, a small single copy (SSC) of 18,791 bp, and a pair of inverted repeats (IRA and IRB) regions of 26,003 bp each. The genome was predicted to encode 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 19 duplicates in the IR regions. In total, 213 SSRs and 44 long repeats were identified in the cp genome. A comparison of two different C. illinoinensis genotypes, ‘Pawnee’ and 87MX3-2.11, obtained 143 SNPs and 74 indels. The highly variable regions such as atpF, clpP, and ndhA genes, and matK-rps16, trnS-trnG, and trnT-psbD intergenic spacers might be helpful for future intraspecific identification. Positive selection was acting on the ccsA and rps12 cp genes based on the Ka/Ks ratios. Phylogenetic analysis indicated that C. illinoinensis forms a sister clade to Asian Carya species, represented by C. kweichowensis and Annamocarya sinensis. Conclusions: The genome information in our study will have significance for further research on the intraspecies identification and genetic improvement of C. illinoinensis.
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Valencia-D J, Murillo-A J, Orozco CI, Parra-O C, Neubig KM. -Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae). PeerJ 2020; 8:e8392. [PMID: 32025370 PMCID: PMC6993752 DOI: 10.7717/peerj.8392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/13/2019] [Indexed: 11/20/2022] Open
Abstract
Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.
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Affiliation(s)
- Janice Valencia-D
- School of Biological Sciences, Southern Illinois University at Carbondale, Carbondale, IL, United States of America
| | - José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Clara Inés Orozco
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Kurt M. Neubig
- School of Biological Sciences, Southern Illinois University at Carbondale, Carbondale, IL, United States of America
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Zhang Z, Zhang Y, Song M, Guan Y, Ma X. Species Identification of Dracaena Using the Complete Chloroplast Genome as a Super-Barcode. Front Pharmacol 2019; 10:1441. [PMID: 31849682 PMCID: PMC6901964 DOI: 10.3389/fphar.2019.01441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 11/12/2019] [Indexed: 01/04/2023] Open
Abstract
The taxonomy and nomenclature of Dracaena plants are much disputed, particularly for several Dracaena species in Asia. However, neither morphological features nor common DNA regions are ideal for identification of Dracaena spp. Meanwhile, although multiple Dracaena spp. are sources of the rare traditional medicine dragon's blood, the Pharmacopoeia of the People's Republic of China has defined Dracaena cochinchinensis as the only source plant. The inaccurate identification of Dracaena spp. will inevitably affect the clinical efficacy of dragon's blood. It is therefore important to find a better method to distinguish these species. Here, we report the complete chloroplast (CP) genomes of six Dracaena spp., D. cochinchinensis, D. cambodiana, D. angustifolia, D. terniflora, D. hokouensis, and D. elliptica, obtained through high-throughput Illumina sequencing. These CP genomes exhibited typical circular tetramerous structure, and their sizes ranged from 155,055 (D. elliptica) to 155,449 bp (D. cochinchinensis). The GC content of each CP genome was 37.5%. Furthermore, each CP genome contained 130 genes, including 84 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. There were no potential coding or non-coding regions to distinguish these six species, but the maximum likelihood tree of the six Dracaena spp. and other related species revealed that the whole CP genome can be used as a super-barcode to identify these Dracaena spp. This study provides not only invaluable data for species identification and safe medical application of Dracaena but also an important reference and foundation for species identification and phylogeny of Liliaceae plants.
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Affiliation(s)
- Zhonglian Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Yue Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Meifang Song
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Yanhong Guan
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Jinghong, China
| | - Xiaojun Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Yang G, Lu H, Wang L, Zhao J, Zeng W, Zhang T. Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken. Genes (Basel) 2019; 10:genes10080628. [PMID: 31434291 PMCID: PMC6723737 DOI: 10.3390/genes10080628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
The chicken is a common type of poultry that is economically important both for its medicinal and nutritional values. Previous studies have found that free-range chickens have more skeletal muscle mass. The methyltransferase-like 21C gene (METTL21C) plays an important role in muscle development; however, there have been few reports on the role of METTL21C in chickens. In this study, we performed a genome-wide identification of chicken METTL21C genes and analyzed their phylogeny, transcriptional expression profile, and real-time quantitative polymerase chain reaction (qPCR). We identified 10 GgMETTL21C genes from chickens, 11 from mice, and 32 from humans, and these genes were divided into six groups, which showed a large amount of variation among these three species. A total of 15 motifs were detected in METTL21C genes, and the intron phase of the gene structure showed that the METTL21C gene family was conservative in evolution. Further, both the transcript data and qPCR showed that a single gene’s (GgMETTL21C3) expression level increased with the muscle development of chickens, indicating that the METTL21C genes are involved in the development of chicken muscles. Our results provide some reference value for the subsequent study of the function of METTL21C.
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Affiliation(s)
- Ge Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Jiarong Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China.
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Xue S, Shi T, Luo W, Ni X, Iqbal S, Ni Z, Huang X, Yao D, Shen Z, Gao Z. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. HORTICULTURE RESEARCH 2019; 6:89. [PMID: 31666958 PMCID: PMC6804877 DOI: 10.1038/s41438-019-0171-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 05/24/2023]
Abstract
Prunus mume Sieb. et Zucc., P. armeniaca L., and P. salicina L. are economically important fruit trees in temperate regions. These species are taxonomically perplexing because of shared interspecific morphological traits and variation, which are mainly attributed to hybridization. The chloroplast is cytoplasmically inherited and often used for evolutionary studies. We sequenced the complete chloroplast genomes of P. mume, P. armeniaca, and P. salicina using Illumina sequencing followed by de novo assembly. The three chloroplast genomes exhibit a typical quadripartite structure with conserved genome arrangement, structure, and moderate divergence. The lengths of the genomes are 157,815, 157,797, and 157,916 bp, respectively. The length of the large single-copy region (LSC) region is 86,113, 86,283, and 86,122 bp, and the length of the SSC region is 18,916, 18,734, and 19,028 bp; the IR region is 26,393, 26,390, and 26,383 bp, respectively. Each of the three chloroplast genomes encodes 133 genes, including 94 protein-coding, 31 tRNA, and eight rRNA genes. Differential gene analysis for the three species revealed that trnY-ATA is a unique gene in P. armeniaca; in contrast, the gene trnI-TAT is only present in P. mume and P. salicina, though the position of the gene in these chloroplast genomes differs. Further comparative analysis of the complete chloroplast genome sequences revealed that the ORF genes and the sequences of linked regions rps16 and atpA, atpH and atpI, trnc-GCA and psbD, ycf3 and atpB, and rpL32 and ndhD are significantly different and may be used as molecular markers in taxonomic studies. Phylogenetic evolution analysis of the three species suggests that P. mume has a closer genetic relationship to P. armeniaca than to P. salicina.
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Affiliation(s)
- Song Xue
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Wenjie Luo
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xiaopeng Ni
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Shahid Iqbal
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xiao Huang
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Dan Yao
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zhijun Shen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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Khan A, Asaf S, Khan AL, Khan A, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Al-Saady N, Al-Rawahi A. Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae. PeerJ 2019; 7:e7260. [PMID: 31328036 PMCID: PMC6625504 DOI: 10.7717/peerj.7260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/05/2019] [Indexed: 02/05/2023] Open
Abstract
Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study.
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Affiliation(s)
- Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Omar Al-Sudairy
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | | | | | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Zhou T, Ruhsam M, Wang J, Zhu H, Li W, Zhang X, Xu Y, Xu F, Wang X. The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae. Front Genet 2019; 10:444. [PMID: 31156705 PMCID: PMC6528182 DOI: 10.3389/fgene.2019.00444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Euphrasia (Orobanchaceae) is a genus which is widely distributed in temperate regions of the southern and northern hemisphere. The taxonomy of Euphrasia is still controversial due to the similarity of morphological characters and a lack of genomic resources. Here, we present the first complete chloroplast (cp) genome of this taxonomically challenging genus. The cp genome of Euphrasia regelii consists of 153,026 bp, including a large single-copy region (83,893 bp), a small single-copy region (15,801 bp) and two inverted repeats (26,666 bp). There are 105 unique genes, including 71 protein-coding genes, 30 tRNA and 4 rRNA genes. Although the structure and gene order is comparable to the one in other angiosperm cp genomes, genes encoding the NAD(P)H dehydrogenase complex are widely pseudogenized due to mutations resulting in frameshifts, and stop codon positions. We detected 36 dispersed repeats, 7 tandem repeats and 65 simple sequence repeat loci in the E. regelii plastome. Comparative analyses indicated that the cp genome of E. regelii is more conserved compared to other hemiparasitic taxa in the Pedicularideae and Buchnereae. No structural rearrangements or loss of genes were detected. Our analyses suggested that three genes (clpP, ycf2 and rps14) were under positive selection and other genes under purifying selection. Phylogenetic analysis of monophyletic Orobanchaceae based on 45 plastomes indicated a close relationship between E. regelii and Neobartsia inaequalis. In addition, autotrophic lineages occupied the earliest diverging branches in our phylogeny, suggesting that autotrophy is the ancestral trait in this parasitic family.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jian Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Honghong Zhu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Wenli Li
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi’an, China
| | - Yucan Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fusheng Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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Xie DF, Yu HX, Price M, Xie C, Deng YQ, Chen JP, Yu Y, Zhou SD, He XJ. Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome. FRONTIERS IN PLANT SCIENCE 2019; 10:460. [PMID: 31114591 PMCID: PMC6503222 DOI: 10.3389/fpls.2019.00460] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/27/2019] [Indexed: 05/25/2023]
Abstract
The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.
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Affiliation(s)
- Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Xi Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuan Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi-Qi Deng
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jun-Pei Chen
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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