1
|
Adamo M, Fochi V, Mucciarelli M. Complete plastome sequence of Narcissus pseudonarcissus L., one of the most iconic European plants. Mitochondrial DNA B Resour 2024; 9:1132-1136. [PMID: 39183765 PMCID: PMC11342812 DOI: 10.1080/23802359.2024.2392758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
Narcissus pseudonarcissus L. is one of the most iconic plants of the European flora. It is a species of great horticultural interest, but also an endangered and protected plant in the wild as a consequence of loss of natural habitats. Complete plastid genome was assembled from next-generation sequencing data obtaining a circular genome of 160,008 bp long assembly. It comprises a pair of inverted repeat regions, a large single-copy region (108,400 bp), and a small single-copy region (16,434 bp). It encodes 131 genes, including 87 protein coding genes, 37 tRNA genes and seven rRNA genes. Phylogeny showed the strict relationship between N. pseudonarcissus and Narcissus poeticus L. The complete plastome will provide a useful genetic resource for future conservation programmes, phylogenetic studies and horticultural applications.
Collapse
Affiliation(s)
- Martino Adamo
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Valeria Fochi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Marco Mucciarelli
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| |
Collapse
|
2
|
Liu L, Li H, Li J, Li X, Hu N, Sun J, Zhou W. Chloroplast genomes of Caragana tibetica and Caragana turkestanica: structures and comparative analysis. BMC PLANT BIOLOGY 2024; 24:254. [PMID: 38594633 PMCID: PMC11003120 DOI: 10.1186/s12870-024-04979-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. RESULTS The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica's sister species is Caragana jubata, whereas C. turkestanica's closest relative is Caragana arborescens. CONCLUSIONS The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.
Collapse
Affiliation(s)
- LiE Liu
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - HongYan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - JiaXin Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - XinJuan Li
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Na Hu
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Jing Sun
- Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Wu Zhou
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China.
| |
Collapse
|
3
|
Xiao F, Zhao Y, Wang X, Jian X. Characterization of the chloroplast genome of Gleditsia species and comparative analysis. Sci Rep 2024; 14:4262. [PMID: 38383559 PMCID: PMC10881578 DOI: 10.1038/s41598-024-54608-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024] Open
Abstract
The genus Gleditsia has significant medicinal and economic value, but information about the chloroplast genomic characteristics of Gleditsia species has been limited. Using the Illumina sequencing, we assembled and annotated the whole chloroplast genomes of seven Gleditsia species (Gleditsia sinensis, Gleditsia japonica var. delavayi (G. delavayi), G. fera, G. japonica, G. microphylla, Fructus Gleditsiae Abnormalis (Zhū Yá Zào), G. microphylla mutant). The assembled genomes revealed that Gleditsia species have a typical circular tetrad structure, with genome sizes ranging from 162,746 to 170,907 bp. Comparative genomic analysis showed that most (65.8-75.8%) of the abundant simple sequence repeats in Gleditsia and Gymnocladus species were located in the large single copy region. The Gleditsia chloroplast genome prefer T/A-ending codons and avoid C/G-ending codons, positive selection was acting on the rpoA, rpl20, atpB, ndhA and ycf4 genes, most of the chloroplast genes of Gleditsia species underwent purifying selection. Expansion and contraction of the inverted repeat (IR)/single copy (SC) region showed similar patterns within the Gleditsia genus. Polymorphism analysis revealed that coding regions were more conserved than non-coding regions, and the IR region was more conserved than the SC region. Mutational hotspots were mostly found in intergenic regions such as "rps16-trnQ", "trnT-trnL", "ndhG-ndhI", and "rpl32-trnL" in Gleditsia. Phylogenetic analysis showed that G. fera is most closely related to G. sinensis,G. japonica and G. delavayi are relatively closely related. Zhū Yá Zào can be considered a bud mutation of the G. sinensis. The albino phenotype of G. microphylla mutant is not caused by variations in the chloroplast genome, and that the occurrence of the albino phenotype may be due to mutations in chloroplast-related genes involved in splicing or localization functions. This study will help us enhance our exploration of the genetic evolution and geographical origins of the Gleditsia genus.
Collapse
Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xueyan Jian
- College of Continuing Education, Yanbian University, Yanji, 133002, Jilin, China
| |
Collapse
|
4
|
Kim KM, Park CY, Lee DH, Jung YH, Kim HM, Na CS. The complete chloroplast genomes of Allium sacculiferum, A. thunbergii, and A. taquetii (Amaryllidaceae) from Korea. Mitochondrial DNA B Resour 2023; 8:1102-1108. [PMID: 37869569 PMCID: PMC10588515 DOI: 10.1080/23802359.2023.2268315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/03/2023] [Indexed: 10/24/2023] Open
Abstract
The genus Allium comprises some of the most commonly consumed food crops worldwide. The chloroplast genomes of A. sacculiferum, A. thunbergii, and A. taquetii are 152,444, 153,459, and 154,056 bp circular molecular genomes, respectively. The annotation results revealed the presence of 132 (89 protein-coding, 35 tRNA, and eight rRNA), 132 (86 protein-coding, 38 tRNA, and eight rRNA), and 132 (86 protein-coding, 38 tRNA, and eight rRNA) genes with 36.78%, 36.83%, and 36.88% total GC content in each genome, respectively. The chloroplast genome of each Allium species contains an 81,254, 82,473, and 83,068 bp LSC region, an 18,176, 18,006, and 17,958 bp SSC region, and a pair of 26,507, 26,490, and 26,515 bp IR regions, respectively. Phylogenetic analysis based on the 21 complete chloroplast genomes indicates that A. sacculiferum is closely related to A. koreanum; A. thunbergii and A taquetii are closely related to A. hookeri. This study shows that the three Allium species are Korean crop wild relatives that may be used to develop new Allium varieties in the future.
Collapse
Affiliation(s)
- Kyeong Min Kim
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Chung Youl Park
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Da Hyun Lee
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Young Ho Jung
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Hyeon Min Kim
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| | - Chae Sun Na
- Wild Plant Seed Research Division, Baekdudaegan National Arboretum, Bonghwa, South Korea
| |
Collapse
|
5
|
Ochar K, Kim SH. Conservation and Global Distribution of Onion ( Allium cepa L.) Germplasm for Agricultural Sustainability. PLANTS (BASEL, SWITZERLAND) 2023; 12:3294. [PMID: 37765458 PMCID: PMC10535454 DOI: 10.3390/plants12183294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Onion (Allium cepa L.) is recognized globally as a crucial vegetable crop, prized not only for its culinary applications but also for its numerous health-promoting properties. With climate change relentlessly exerting mounting challenges to agriculture, the preservation and deployment of onion germplasm has become critical to ensuring sustainable agriculture and safeguarding food security. Global onion germplasm collections function as repositories of genetic diversity, holding within them an extensive array of valuable traits or genes. These can be harnessed to develop varieties resilient to climate adversities. Therefore, detailed information concerning onion germplasm collections from various geographical regions can bolster their utility. Furthermore, an amplified understanding of the importance of fostering international and inter-institutional collaborations becomes essential. Sharing and making use of onion genetic resources can provide viable solutions to the looming agricultural challenges of the future. In this review, we have discussed the preservation and worldwide distribution of onion germplasm, along with its implications for agricultural sustainability. We have also underscored the importance of international and interinstitutional collaboration in onion germplasm collecting and conservation for agricultural sustainability.
Collapse
Affiliation(s)
- Kingsley Ochar
- Council for Scientific and Industrial Research, Plant Genetic Resources Research Institute, Bunso P.O. Box 7, Ghana;
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 5487, Republic of Korea
| |
Collapse
|
6
|
Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
Collapse
Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|
7
|
Xu XM, Wei Z, Sun JZ, Zhao QF, Lu Y, Wang ZL, Zhu SX. Phylogeny of Leontopodium (Asteraceae) in China-with a reference to plastid genome and nuclear ribosomal DNA. FRONTIERS IN PLANT SCIENCE 2023; 14:1163065. [PMID: 37583593 PMCID: PMC10425225 DOI: 10.3389/fpls.2023.1163065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023]
Abstract
The infrageneric taxonomy system, species delimitation, and interspecies systematic relationships of Leontopodium remain controversial and complex. However, only a few studies have focused on the molecular phylogeny of this genus. In this study, the characteristics of 43 chloroplast genomes of Leontopodium and its closely related genera were analyzed. Phylogenetic relationships were inferred based on chloroplast genomes and nuclear ribosomal DNA (nrDNA). Finally, together with the morphological characteristics, the relationships within Leontopodium were identified and discussed. The results showed that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved in terms of gene number, gene order, and GC content. The most remarkable differences among the three genera were the length of the complete chloroplast genome, large single-copy region, small single-copy region, and inverted repeat region. In addition, the chloroplast genome structure of Leontopodium exhibited high consistency and was obviously different from that of Filago and Gamochaeta in some regions, such as matk, trnK (UUU)-rps16, petN-psbM, and trnE (UUC)-rpoB. All the phylogenetic trees indicated that Leontopodium was monophyletic. Except for the subgeneric level, our molecular phylogenetic results were inconsistent with the previous taxonomic system, which was based on morphological characteristics. Nevertheless, we found that the characteristics of the leaf base, stem types, and carpopodium base were phylogenetically correlated and may have potential value in the taxonomic study of Leontopodium. In the phylogenetic trees inferred using complete chloroplast genomes, the subgen. Leontopodium was divided into two clades (Clades 1 and 2), with most species in Clade 1 having herbaceous stems, amplexicaul, or sheathed leaves, and constricted carpopodium; most species in Clade 2 had woody stems, not amplexicaul and sheathed leaves, and not constricted carpopodium.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
8
|
Xu XM, Liu DH, Zhu SX, Wang ZL, Wei Z, Liu QR. Phylogeny of Trigonotis in China-with a special reference to its nutlet morphology and plastid genome. PLANT DIVERSITY 2023; 45:409-421. [PMID: 37601540 PMCID: PMC10435912 DOI: 10.1016/j.pld.2023.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 08/22/2023]
Abstract
The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia. China has the largest number of Trigonotis species in the world, with a total of 44 species, of which 38 are endemic. Nutlet morphology is useful for the taxonomic delimitation of Trigonotis. However, there are still controversial circumscriptions of nutlet shape in some species. In previous studies, interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa, which possibly led to erroneous or incomplete conclusions. In this study, the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes (29 taxa) were investigated and analyzed. Then, the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes. To the best of our knowledge, this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis. Based on nutlet morphology, Trigonotis can be divided into two groups: Group 1, hemispherical or oblique tetrahedron with carpopodiums, and Group 2, inverted tetrahedron without carpopodiums. The chloroplast genome of Trigonotis exhibited a typical quadripartite structure, including 84-86 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes, with a total length of 147,247-148,986 bp. Genes in the junctions were well conserved in Trigonotis, similar to those in other Boraginaceae s.str. species. Furthermore, Trigonotis chloroplast genomes showed relatively high diversity, with more conserved genic regions than intergenic regions; in addition, we detected 14 hot spots (Pi > 0.005) in non-coding regions. Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species. Specifically, Trigonotis was divided into two clades with strong support: one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts, whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts. Our results may inform future taxonomic, phylogenetic, and evolutionary studies on Boraginaceae.
Collapse
Affiliation(s)
- Xue-Min Xu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Dan-Hui Liu
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shi-Xin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhen-Long Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Quan-Ru Liu
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
9
|
Bhowmick BK, Sarkar S, Roychowdhury D, Patil SD, Lekhak MM, Ohri D, Rama Rao S, Yadav SR, Verma RC, Dhar MK, Raina SN, Jha S. Allium cytogenetics: a critical review on the Indian taxa. COMPARATIVE CYTOGENETICS 2023; 17:129-156. [PMID: 37304149 PMCID: PMC10252142 DOI: 10.3897/compcytogen.17.98903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/28/2023] [Indexed: 06/13/2023]
Abstract
The genus Allium Linnaeus, 1753 (tribe Allieae) contains about 800 species worldwide of which almost 38 species are reported in India, including the globally important crops (onion, garlic, leek, shallot) and many wild species. A satisfactory chromosomal catalogue of Allium species is missing which has been considered in the review for the species occurring in India. The most prominent base number is x=8, with few records of x=7, 10, 11. The genome size has sufficient clues for divergence, ranging from 7.8 pg/1C to 30.0 pg/1C in diploid and 15.16 pg/1C to 41.78 pg/1C in polyploid species. Although the karyotypes are seemingly dominated by metacentrics, substantial variation in nucleolus organizing regions (NORs) is noteworthy. The chromosomal rearrangement between A.cepa Linnaeus, 1753 and its allied species has paved way to appreciate genomic evolution within Allium. The presence of a unique telomere sequence and its conservation in Allium sets this genus apart from all other Amaryllids and supports monophyletic origin. Any cytogenetic investigation regarding NOR variability, telomere sequence and genome size in the Indian species becomes the most promising field to decipher chromosome evolution against the background of species diversity and evolution, especially in the Indian subcontinent.
Collapse
Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata- 700006, West Bengal, IndiaDepartment of Botany, Scottish Church CollegeKolkataIndia
| | - Sayantika Sarkar
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
| | - Dipasree Roychowdhury
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
| | - Sayali D. Patil
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - Manoj M. Lekhak
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - Deepak Ohri
- Amity Institute of Biotechnology, Research Cell, Amity University Uttar Pradesh, Lucknow Campus, Lucknow- 226028, Uttar Pradesh, IndiaAmity University Uttar PradeshLucknowIndia
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya- 793022, IndiaNorth-Eastern Hill UniversityShillongIndia
| | - S. R. Yadav
- Angiosperm Taxonomy Laboratory, Department of Botany, Shivaji University, Kolhapur, Maharashtra- 416004, IndiaShivaji UniversityKolhapurIndia
| | - R. C. Verma
- School of Studies in Botany, Vikram University, Ujjain, Madhya Pradesh 456010, IndiaVikram UniversityUjjainIndia
| | - Manoj K. Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir- 180006, IndiaUniversity of JammuJammuIndia
| | - S. N. Raina
- Amity Institute of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh- 201313, IndiaAmity UniversityNoidaIndia
| | - Sumita Jha
- Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata- 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
| |
Collapse
|
10
|
Alshegaihi RM, Mansour H, Alrobaish SA, Al Shaye NA, Abd El-Moneim D. The First Complete Chloroplast Genome of Cordia monoica: Structure and Comparative Analysis. Genes (Basel) 2023; 14:genes14050976. [PMID: 37239336 DOI: 10.3390/genes14050976] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
Collapse
Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| |
Collapse
|
11
|
Yen LT, Kousar M, Park J. Comparative Analysis of Chloroplast Genome of Desmodium stryacifolium with Closely Related Legume Genome from the Phaseoloid Clade. Int J Mol Sci 2023; 24:ijms24076072. [PMID: 37047046 PMCID: PMC10094673 DOI: 10.3390/ijms24076072] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Desmodium styracifolium is a medicinal plant from the Desmodieae tribe, also known as Grona styracifolia. Its role in the treatment of urolithiasis, urinary infections, and cholelithiasis has previously been widely documented. The complete chloroplast genome sequence of D. Styracifolium is 149,155 bp in length with a GC content of 35.2%. It is composed of a large single copy (LSC) of 82,476 bp and a small single copy (SSC) of 18,439 bp, which are separated by a pair of inverted repeats (IR) of 24,120 bp each and has 128 genes. We performed a comparative analysis of the D. styracifolium cpDNA with the genome of previously investigated members of the Sesamoidea tribe and on the outgroup from its Phaseolinae sister tribe. The size of all seven cpDNAs ranged from 148,814 bp to 151,217 bp in length due to the contraction and expansion of the IR/SC boundaries. The gene orientation of the SSC region in D. styracifolium was inverted in comparison with the other six studied species. Furthermore, the sequence divergence of the IR regions was significantly lower than that of the LSC and the SSC, and five highly divergent regions, trnL-UAA-trnT-UGU, psaJ-ycf4, psbE-petL, rpl36-rps8, and rpl32-trnL-UGA, were identified that could be used as valuable molecular markers in future taxonomic studies and phylogenetic constructions.
Collapse
Affiliation(s)
- Le-Thi Yen
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Muniba Kousar
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Joonho Park
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| |
Collapse
|
12
|
Yang J, Kim SH, Gil HY, Choi HJ, Kim SC. New insights into the phylogenetic relationships among wild onions ( Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1124277. [PMID: 37025138 PMCID: PMC10070991 DOI: 10.3389/fpls.2023.1124277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
The genus Allium, with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within Allium have long been not resolved. Based on 76 species of Allium (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera Anguinum and Rhizirideum. We retrieved the three major evolutionary lines within Allium and found that the two subgenera Anguinum and Rhizirideum are monophyletic whereas others are highly polyphyletic (e.g., Allium, Cepa, Polyprason, and Melanocrommyum). Within the subgenus Anguinum, two strongly supported sublineages in East Asian and Eurasian-American were found. Allium tricoccum in North America belonged to the Eurasian clade. The distinct taxonomic status of A. ulleungense and its sister taxon were further determined. In subg. Rhizirideum, the Ulleung Island endemic A. dumebuchum shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic A. minus. Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian A. macrostemon (subg. Allium) and sister relationship between A. condensatum and A. chinense was suggested.
Collapse
Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea
| | - Seon-Hee Kim
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Republic of Korea
| | - Hyeok-Jae Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| |
Collapse
|
13
|
Zhang SD, Yan K, Ling LZ. Characterization and phylogenetic analyses of ten complete plastomes of Spiraea species. BMC Genomics 2023; 24:137. [PMID: 36944915 PMCID: PMC10029230 DOI: 10.1186/s12864-023-09242-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Spiraea is a genus of deciduous shrubs that contains 80-120 species, is mainly distributed in the Northern Hemisphere and has diversified in East Asia. Spiraea species are cultivated as ornamental plants and some are used in traditional herbal medicine. Based on morphological characteristics and genetic markers, phylogenetic classification exhibits low discriminatory power. RESULTS In present study, we assembled and characterized the chloroplast (cp) genomes of ten Spiraea species and comparatively analysed with five reported cp genomes of this genus. The cp genomes of the fifteen Spiraea species, ranging from 155,904 to 158,637 bp in length, were very conserved and no structural rearrangements occurred. A total of 85 protein-coding genes (PCGs), 37 tRNAs and 8 rRNAs were annotated. We also examined 1,010 simple sequence repeat (SSR) loci, most of which had A/T base preference. Comparative analysis of cp genome demonstrated that single copy and non-coding regions were more divergent than the inverted repeats (IRs) and coding regions and six mutational hotspots were detected. Selection pressure analysis showed that all PCGs were under purifying selection. Phylogenetic analysis based on the complete cp genome data showed that Spiraea formed a monophyletic group and was further divided into two major clades. Infrageneric classification in each clade was supported with a high resolution value. Moreover, the phylogenetic trees based on each individual mutational hotspot segment and their combined dataset also consisted of two major clades, but most of the phylogenetic relationships of interspecies were not well supported. CONCLUSIONS Although the cp genomes of Spiraea species exhibited high conservation in genome structure, gene content and order, a large number of polymorphism sites and several mutation hotspots were identified in whole cp genomes, which might be sufficiently used as molecular markers to distinguish Spiraea species. Phylogenetic analysis based on the complete cp genome indicated that infrageneric classification in two major clades was supported with high resolution values. Therefore, the cp genome data of the genus Spiraea will be effective in resolving the phylogeny in this genus.
Collapse
Affiliation(s)
- Shu-Dong Zhang
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China
| | - Kai Yan
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China.
| | - Li-Zhen Ling
- School of Biological Science and Technology, Liupanshui Normal University, Liupanshui, Guizhou, China.
| |
Collapse
|
14
|
Characterization of the Plastid Genome of the Vulnerable Endemic Indosasa lipoensis and Phylogenetic Analysis. DIVERSITY 2023. [DOI: 10.3390/d15020197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Indosasa lipoensis, an ornamental garden plant, belongs to the Indosasa genus of the subfamily Bambooaceae within Poaceae. Indosasa lipoensis is endangered and requires protection owing to its relatively narrow distribution area. Chloroplast (cp) genome offers a novel awareness of the evolutionary and genetic variation of higher plants. Herein, we assembled and elucidated the complete cp genome of I. lipoensis, and compared it with four previously published cp genomes from this genus. The I. lipoensis cp genome was 139,655 bp in size, with a typical quadripartite structure, encompassing a large single-copy region (LSC, 83,256 bp), a small single-copy region (SSC, 12,809 bp), and a pair of inverted repeat regions (IR, 21,795 bp). The cp genome consisted of 130 genes with 84 protein-coding genes (CDS), 38 tRNA genes, and 8 rRNA genes. The plastomes were highly conservative, compared to other bamboo species, and exhibited similar patterns of codon usage, number of repeat sequences, and expansion and contraction of the IR boundary. Five hypervariable hotspots were identified as potential DNA barcodes, namely rbcL, petA, petB, trnL-UAG, and ndhE-ndhI, respectively. Phylogenetic analysis based on the complete cp genomes revealed, with high resolution, that I. lipoensis and I. gigantea were most closely related. Overall, these results provided valuable characterization for the future conservation, genetic evaluation, and the breeding of I. lipoensis.
Collapse
|
15
|
Wanichthanarak K, Nookaew I, Pasookhush P, Wongsurawat T, Jenjaroenpun P, Leeratsuwan N, Wattanachaisaereekul S, Visessanguan W, Sirivatanauksorn Y, Nuntasaen N, Kuhakarn C, Reutrakul V, Ajawatanawong P, Khoomrung S. Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae. BMC PLANT BIOLOGY 2023; 23:59. [PMID: 36707785 PMCID: PMC9883906 DOI: 10.1186/s12870-023-04074-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. RESULTS The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. CONCLUSIONS In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.
Collapse
Affiliation(s)
- Kwanjeera Wanichthanarak
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Phongthana Pasookhush
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Namkhang Leeratsuwan
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | | | - Wonnop Visessanguan
- Functional Ingredients and Food Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), Phathumthani, 12120, Thailand
| | - Yongyut Sirivatanauksorn
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Narong Nuntasaen
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, 10900, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Vichai Reutrakul
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Pravech Ajawatanawong
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Sakda Khoomrung
- Metabolomics and Systems Biology, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| |
Collapse
|
16
|
Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum. Sci Rep 2022; 12:21676. [PMID: 36522492 PMCID: PMC9755143 DOI: 10.1038/s41598-022-26354-0] [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: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.
Collapse
|
17
|
Targeted Metabolome Profiling of Indonesian Shallots and Japanese Long-Day/Short-Day Bulb Onions. Metabolites 2022; 12:metabo12121260. [PMID: 36557300 PMCID: PMC9783499 DOI: 10.3390/metabo12121260] [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: 10/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/16/2022] Open
Abstract
In this study, targeted metabolome analysis was applied to identify the discriminative metabolites between Indonesian shallot landraces, Japanese long-day onion (LDO) varieties, and Japanese short-day onion (SDO) varieties. In total, 172 metabolite signal intensities were subjected to multivariate PLS-DA, VIP, and random forest modeling to gain further insight into genotype-specific metabolites. PLS-DA divides the examined genotypes into three different clusters, implying that shallot landraces exhibited a distinct metabolite profile compared with Japanese LDO and SDO varieties. The PLS-DA, VIP, and random forest results indicated that the shallot and LDO are richer in metabolite constituents in comparison with the SDO. Specifically, amino acids and organosulfur compounds were the key characteristic metabolites in shallot and LDO genotypes. The analysis of S-alk(en)yl-L-cysteine sulfoxide (ACSO) compounds showed higher accumulation in the shallot landraces relative to LDO and SDO varieties, which explains the stronger pungency and odor in shallots. In addition, the LDO showed higher ACSO content compared with the SDO, implying that long-day cultivation might enhance sulfur assimilation in the Japanese onion. The LDO 'Super Kitamomiji' and the shallots 'Probolinggo' and 'Thailand' showed higher ACSO content than other varieties, making it useful for Allium breeding to improve the flavor and stress tolerance of onions.
Collapse
|
18
|
Park YS, Kang JS, Park JY, Shim H, Yang HO, Kang JH, Yang TJ. Analysis of the complete plastomes and nuclear ribosomal DNAs from Euonymus hamiltonianus and its relatives sheds light on their diversity and evolution. PLoS One 2022; 17:e0275590. [PMID: 36197898 PMCID: PMC9534445 DOI: 10.1371/journal.pone.0275590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Euonymus hamiltonianus and its relatives (Celastraceae family) are used for ornamental and medicinal purposes. However, species identification in Euonymus is difficult due to their morphological diversity. Using plastid genome (plastome) data, we attempt to reveal phylogenetic relationship among Euonymus species and develop useful markers for molecular identification. We assembled the plastome and nuclear ribosomal DNA (nrDNA) sequences from five Euonymus lines collected from South Korea: three Euonymus hamiltonianus accessions, E. europaeus, and E. japonicus. We conducted an in-depth comparative analysis using ten plastomes, including other publicly available plastome data for this genus. The genome structures, gene contents, and gene orders were similar in all Euonymus plastomes in this study. Analysis of nucleotide diversity revealed six divergence hotspots in their plastomes. We identified 339 single nucleotide polymorphisms and 293 insertion or deletions among the four E. hamiltonianus plastomes, pointing to abundant diversity even within the same species. Among 77 commonly shared genes, 9 and 33 were identified as conserved genes in the genus Euonymus and E. hamiltonianus, respectively. Phylogenetic analysis based on plastome and nrDNA sequences revealed the overall consensus and relationships between plastomes and nrDNAs. Finally, we developed six barcoding markers and successfully applied them to 31 E. hamiltonianus lines collected from South Korea. Our findings provide the molecular basis for the classification and molecular taxonomic criteria for the genus Euonymus (at least in Korea), which should aid in more objective classification within this genus. Moreover, the newly developed markers will be useful for understanding the species delimitation of E. hamiltonianus and closely related species.
Collapse
Affiliation(s)
- Young Sang Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Jee Young Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
| | - Hyun Ok Yang
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Korea
| | | | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics & Breeding Institute, College of Agriculture & Life Sciences, Seoul National University, Seoul, Korea
- * E-mail:
| |
Collapse
|
19
|
Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species ( Iris Series Chinenses, Iridaceae). Int J Mol Sci 2022; 23:ijms231810929. [PMID: 36142840 PMCID: PMC9504294 DOI: 10.3390/ijms231810929] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 12/16/2022] Open
Abstract
The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.
Collapse
|
20
|
Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships. Genes (Basel) 2022; 13:genes13091550. [PMID: 36140718 PMCID: PMC9498446 DOI: 10.3390/genes13091550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.
Collapse
|
21
|
Comparison Analysis Based on Complete Chloroplast Genomes and Insights into Plastid Phylogenomic of Four Iris Species. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2194021. [PMID: 35937412 PMCID: PMC9348943 DOI: 10.1155/2022/2194021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/06/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022]
Abstract
Iris species, commonly known as rainbow flowers because of their attractive flowers, are extensively grown in landscape gardens. A few species, including Belamcanda chinensis, the synonym of I. domestica and I. tectorum, are known for their medicinal properties. However, research on the genomes and evolutionary relationships of Iris species is scarce. In the current study, the complete chloroplast (CP) genomes of I. tectorum, I. dichotoma, I. japonica, and I. domestica were sequenced and compared for their identification and relationship. The CP genomes of the four Iris species were circular quadripartite with similar lengths, GC contents, and codon usages. A total of 113 specific genes were annotated, including the ycf1 pseudogene in all species and rps19 in I. japonica alone. All the species had mononucleotide (A/T) simple sequence repeats (SSRs) and long forward and palindromic repeats in their genomes. A comparison of the CP genomes based on mVISTA and nucleotide diversity (Pi) identified three highly variable regions (ndhF-rpl32, rps15-ycf1, and rpl16). Phylogenetic analysis based on the complete CP genomes concluded that I. tectorum is a sister of I. japonica, and the subgenus Pardanthopsis with several I. domestica clustered into one branch is a sister of I. dichotoma. These findings confirm the feasibility of superbarcodes (complete CP genomes) for Iris species authentication and could serve as a resource for further research on Iris phylogeny.
Collapse
|
22
|
Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. Genes (Basel) 2022; 13:genes13071279. [PMID: 35886061 PMCID: PMC9324613 DOI: 10.3390/genes13071279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 12/03/2022] Open
Abstract
With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions’ fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species.
Collapse
|
23
|
Guo H, Wang L, Xu W, Huo Z, Yang P, Zhang Q, Wang H, Li P, Lu X. The complete chloroplast genome sequence of Cyathula officinalis and comparative analysis with four related species. Gene 2022; 839:146728. [PMID: 35850203 DOI: 10.1016/j.gene.2022.146728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/14/2022] [Accepted: 07/08/2022] [Indexed: 11/17/2022]
Abstract
Cyathula officinalis is a medicinal and edible herb, which can remove blood stasis, stimulate menstrual flow, and ease joint movement. In this study, the complete chloroplast genome of Cyathula officinalis was sequenced, assembled, and analyzed. Compared with the chloroplast genomes of Cyathula capitata, Achyranthes bidentata, Achyranthes longifolianine and Achyranthes aspera, the basic characteristics, codon usage bias, repeat sequences, simple sequence repeats, and phylogenetic tree were analyzed. In addition, according to nucleotide diversity analysis and sequence alignment, DNA barcoding and allele-specific PCR primers were designed to identify and distinguish Cyathula officinalis from its fake drugs, which has effectively practical significance for the authentication of "Chuan Niuxi" crude drug in the market.
Collapse
Affiliation(s)
- Huijun Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Long Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Wenbo Xu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Ziting Huo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Qianwen Zhang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Huiying Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Medicine, China Pharmaceutical University, Nanjing 211198, China.
| |
Collapse
|
24
|
Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology. Sci Rep 2022; 12:9424. [PMID: 35676304 PMCID: PMC9177672 DOI: 10.1038/s41598-022-13528-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 11/12/2022] Open
Abstract
Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.
Collapse
|
25
|
Comparative Chloroplast Genome Analysis of Wax Gourd (Benincasa hispida) with Three Benincaseae Species, Revealing Evolutionary Dynamic Patterns and Phylogenetic Implications. Genes (Basel) 2022; 13:genes13030461. [PMID: 35328015 PMCID: PMC8954987 DOI: 10.3390/genes13030461] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/01/2022] [Indexed: 12/13/2022] Open
Abstract
Benincasa hispida (wax gourd) is an important Cucurbitaceae crop, with enormous economic and medicinal importance. Here, we report the de novo assembly and annotation of the complete chloroplast genome of wax gourd with 156,758 bp in total. The quadripartite structure of the chloroplast genome comprises a large single-copy (LSC) region with 86,538 bp and a small single-copy (SSC) region with 18,060 bp, separated by a pair of inverted repeats (IRa and IRb) with 26,080 bp each. Comparison analyses among B. hispida and three other species from Benincaseae presented a significant conversion regarding nucleotide content, genome structure, codon usage, synonymous and non-synonymous substitutions, putative RNA editing sites, microsatellites, and oligonucleotide repeats. The LSC and SSC regions were found to be much more varied than the IR regions through a divergent analysis of the species within Benincaseae. Notable IR contractions and expansions were observed, suggesting a difference in genome size, gene duplication and deletion, and the presence of pseudogenes. Intronic gene sequences, such as trnR-UCU–atpA and atpH–atpI, were observed as highly divergent regions. Two types of phylogenetic analysis based on the complete cp genome and 72 genes suggested sister relationships between B. hispida with the Citrullus, Lagenaria, and Cucumis. Variations and consistency with previous studies regarding phylogenetic relationships are discussed. The cp genome of B. hispida provides valuable genetic information for the detection of molecular markers, research on taxonomic discrepancies, and the inference of the phylogenetic relationships of Cucurbitaceae.
Collapse
|
26
|
Wambugu PW, Henry R. Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies. Mol Ecol 2022; 31:2207-2222. [PMID: 35170117 PMCID: PMC9303585 DOI: 10.1111/mec.16402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/27/2022]
Abstract
The last decade has witnessed huge technological advances in genomics, particularly in DNA sequencing. Here, we review the actual and potential application of genomics in supporting in situ conservation of crop wild relatives (CWRs). In addition to helping in prioritization of protection of CWR taxa and in situ conservation sites, genome analysis is allowing the identification of novel alleles that need to be prioritized for conservation. Genomics is enabling the identification of potential sources of important adaptive traits that can guide the establishment or enrichment of in situ genetic reserves. Genomic tools also have the potential for developing a robust framework for monitoring and reporting genome‐based indicators of genetic diversity changes associated with factors such as land use or climate change. These tools have been demonstrated to have an important role in managing the conservation of populations, supporting sustainable access and utilization of CWR diversity, enhancing accelerated domestication of new crops and forensic genomics thus preventing misappropriation of genetic resources. Despite this great potential, many policy makers and conservation managers have failed to recognize and appreciate the need to accelerate the application of genomics to support the conservation and management of biodiversity in CWRs to underpin global food security. Funding and inadequate genomic expertise among conservation practitioners also remain major hindrances to the widespread application of genomics in conservation.
Collapse
Affiliation(s)
- Peterson W Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, 00100, Nairobi, Kenya
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
27
|
Characterization of the complete chloroplast genome of Zephyranthes phycelloides ( Amaryllidaceae, tribe Hippeastreae) from Atacama region of Chile. Saudi J Biol Sci 2022; 29:650-659. [PMID: 35002462 PMCID: PMC8716934 DOI: 10.1016/j.sjbs.2021.10.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Sporadic rains in the Atacama Desert reveal a high biodiversity of plant species that only occur there. One of these rare species is the “Red añañuca” (Zephyranthes phycelloides), formerly known as Rhodophiala phycelloides. Many species of Zephyranthes in the Atacama Desert are dangerously threatened, due to massive extraction of bulbs and cutting of flowers. Therefore, studies of the biodiversity of these endemic species, which are essential for their conservation, should be conducted sooner rather than later. There are some chloroplast genomes available for Amaryllidaceae species, however there is no complete chloroplast genome available for any of the species of Zephyranthes subgenus Myostemma. The aim of the present work was to characterize and analyze the chloroplast of Z. phycelloides by NGS sequencing. The chloroplast genome of the Z. phycelloides consists of 158,107 bp, with typical quadripartite structures: a large single copy (LSC, 86,129 bp), a small single copy (SSC, 18,352 bp), and two inverted repeats (IR, 26,813 bp). One hundred thirty-seven genes were identified: 87 coding genes, 8 rRNA, 38 tRNA and 4 pseudogenes. The number of SSRs was 64 in Z. phycelloides and a total of 43 repeats were detected. The phylogenetic analysis of Z. phycelloides shows a distinct subclade with respect to Z. mesochloa. The average nucleotide variability (Pi) between Z. phycelloides and Z. mesochloa was of 0.02000, and seven loci with high variability were identified: psbA, trnSGCU-trnGUCC, trnDGUC-trnYGUA, trnLUAA-trnFGAA, rbcL, psbE-petL and ndhG-ndhI. The differences between the species are furthermore confirmed by the high amount of SNPs between these two species. Here, we report for the first time the complete cp genome of one species of the Zephyranthes subgenus Myostemma, which can be used for phylogenetic and population genomic studies.
Collapse
|
28
|
Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
Collapse
Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
29
|
Song Y, Feng L, Alyafei MAM, Jaleel A, Ren M. Function of Chloroplasts in Plant Stress Responses. Int J Mol Sci 2021; 22:ijms222413464. [PMID: 34948261 PMCID: PMC8705820 DOI: 10.3390/ijms222413464] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 12/24/2022] Open
Abstract
The chloroplast has a central position in oxygenic photosynthesis and primary metabolism. In addition to these functions, the chloroplast has recently emerged as a pivotal regulator of plant responses to abiotic and biotic stress conditions. Chloroplasts have their own independent genomes and gene-expression machinery and synthesize phytohormones and a diverse range of secondary metabolites, a significant portion of which contribute the plant response to adverse conditions. Furthermore, chloroplasts communicate with the nucleus through retrograde signaling, for instance, reactive oxygen signaling. All of the above facilitate the chloroplast’s exquisite flexibility in responding to environmental stresses. In this review, we summarize recent findings on the involvement of chloroplasts in plant regulatory responses to various abiotic and biotic stresses including heat, chilling, salinity, drought, high light environmental stress conditions, and pathogen invasions. This review will enrich the better understanding of interactions between chloroplast and environmental stresses, and will lay the foundation for genetically enhancing plant-stress acclimatization.
Collapse
Affiliation(s)
- Yun Song
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China;
| | - Li Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China;
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
| | - Mohammed Abdul Muhsen Alyafei
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.A.M.A.); (A.J.)
| | - Abdul Jaleel
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates; (M.A.M.A.); (A.J.)
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610213, China;
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-(13)-527313471
| |
Collapse
|
30
|
Zhang Y, Song MF, Li Y, Sun HF, Tang DY, Xu AS, Yin CY, Zhang ZL, Zhang LX. Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis. FRONTIERS IN PLANT SCIENCE 2021; 12:705892. [PMID: 34975932 PMCID: PMC8714959 DOI: 10.3389/fpls.2021.705892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/18/2021] [Indexed: 06/03/2023]
Abstract
Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine-cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Zhong-Lian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Li-Xia Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| |
Collapse
|
31
|
Yu Y, Han Y, Peng Y, Tian Z, Zeng P, Zong H, Zhou T, Cai J. Comparative and phylogenetic analyses of eleven complete chloroplast genomes of Dipterocarpoideae. Chin Med 2021; 16:125. [PMID: 34823565 PMCID: PMC8620154 DOI: 10.1186/s13020-021-00538-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In South-east Asia, Dipterocarpoideae is predominant in most mature forest communities, comprising around 20% of all trees. As large quantity and high quality wood are produced in many species, Dipterocarpoideae plants are the most important and valuable source in the timber market. The d-borneol is one of the essential oil components from Dipterocarpoideae (for example, Dryobalanops aromatica or Dipterocarpus turbinatus) and it is also an important traditional Chinese medicine (TCM) formulation known as "Bingpian" in Chinese, with antibacterial, analgesic and anti-inflammatory effects and can enhance anticancer efficiency. METHODS In this study, we analyzed 20 chloroplast (cp) genomes characteristics of Dipterocarpoideae, including eleven newly reported genomes and nine cp genomes previously published elsewhere, then we explored the chloroplast genomic features, inverted repeats contraction and expansion, codon usage, amino acid frequency, the repeat sequences and selective pressure analyses. At last, we constructed phylogenetic relationships of Dipterocarpoideae and found the potential barcoding loci. RESULTS The cp genome of this subfamily has a typical quadripartite structure and maintains a high degree of consistency among species. There were slightly more tandem repeats in cp genomes of Dipterocarpus and Vatica, and the psbH gene was subjected to positive selection in the common ancestor of all the 20 species of Dipterocarpoideae compared with three outgroups. Phylogenetic tree showed that genus Shorea was not a monophyletic group, some Shorea species and genus Parashorea are placed in one clade. In addition, the rpoC2 gene can be used as a potential marker to achieve accurate and rapid species identification in subfamily Dipterocarpoideae. CONCLUSIONS Dipterocarpoideae had similar cp genomic features and psbM, rbcL, psbH may function in the growth of Dipterocarpoideae. Phylogenetic analysis suggested new taxon treatment is needed for this subfamily indentification. In addition, rpoC2 is potential to be a barcoding gene to TCM distinguish.
Collapse
Affiliation(s)
- Yang Yu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078 Macau, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, China
| |
Collapse
|
32
|
Li DM, Li J, Wang DR, Xu YC, Zhu GF. Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC PLANT BIOLOGY 2021; 21:558. [PMID: 34814832 PMCID: PMC8611967 DOI: 10.1186/s12870-021-03315-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. RESULTS Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda 'Red Leaf', Kaempferia rotunda 'Silver Diamonds' and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630-163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172-88,632 bp), a small single copy (SSC, 15,393-15,917 bp) and a pair of inverted repeats (IRs, 29,673-29,833 bp). The genomes contain 111-113 different genes, including 79 protein coding genes, 28-30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + "the Kaempferia clade" consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. CONCLUSIONS Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.
Collapse
Affiliation(s)
- Dong-Mei Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dai-Rong Wang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ye-Chun Xu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| |
Collapse
|
33
|
Könyves K, Bilsborrow J, Christodoulou MD, Culham A, David J. Comparative plastomics of Amaryllidaceae: inverted repeat expansion and the degradation of the ndh genes in Strumaria truncata Jacq. PeerJ 2021; 9:e12400. [PMID: 34824912 PMCID: PMC8592052 DOI: 10.7717/peerj.12400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Amaryllidaceae is a widespread and distinctive plant family contributing both food and ornamental plants. Here we present an initial survey of plastomes across the family and report on both structural rearrangements and gene losses. Most plastomes in the family are of similar gene arrangement and content however some taxa have shown gains in plastome length while in several taxa there is evidence of gene loss. Strumaria truncata shows a substantial loss of ndh family genes while three other taxa show loss of cemA, which has been reported only rarely. Our sparse sampling of the family has detected sufficient variation to suggest further sampling across the family could be a rich source of new information on plastome variation and evolution.
Collapse
Affiliation(s)
- Kálmán Könyves
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Jordan Bilsborrow
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | | | - Alastair Culham
- Herbarium, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - John David
- Royal Horticultural Society Garden Wisley, Woking, United Kingdom
| |
Collapse
|
34
|
Park I, Song JH, Yang S, Chae S, Moon BC. Plastid Phylogenomic Data Offers Novel Insights Into the Taxonomic Status of the Trichosanthes kirilowii Complex (Cucurbitaceae) in South Korea. FRONTIERS IN PLANT SCIENCE 2021; 12:559511. [PMID: 34386020 PMCID: PMC8353159 DOI: 10.3389/fpls.2021.559511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Trichosanthes is a genus in Cucurbitaceae comprising 90-100 species. Trichosanthes species are valuable as herbaceous medicinal ingredients. The fruits, seeds, and roots of species such as T. kirilowii and T. rosthornii are used in Korean traditional herbal medicines. T. rosthornii is only found in China, whereas in South Korea two varieties, T. kirilowii var. kirilowii and T. kirilowii var. japonica, are distributed. T. kirilowii var. kirilowii and T. kirilowii var. japonica have different fruit and leaf shapes but are recognized as belonging to the same species. Furthermore, although its members have herbal medicine applications, genomic information of the genus is still limited. The broad goals of this study were (i) to evaluate the taxonomy of Trichosanthes using plastid phylogenomic data and (ii) provide molecular markers specific for T. kirilowii var. kirilowii and T. kirilowii var. japonica, as these have differences in their pharmacological effectiveness and thus should not be confused and adulterated. Comparison of five Trichosanthes plastid genomes revealed locally divergent regions, mainly within intergenic spacer regions (trnT-UGU-trnL-UAA: marker name Tri, rrn4.5-rrn5: TRr, trnE-UUC-trnT-GGU: TRtt). Using these three markers as DNA-barcodes for important herbal medicine species in Trichosanthes, the identity of Trichosanthes material in commercial medicinal products in South Korea could be successfully determined. Phylogenetic analysis of the five Trichosanthes species revealed that the species are clustered within tribe Sicyoeae. T. kirilowii var. kirilowii and T. rosthornii formed a clade with T. kirilowii var. japonica as their sister group. As T. kirilowii in its current circumscription is paraphyletic and as the two varieties can be readily distinguished morphologically (e.g., in leaf shape), T. kirilowii var. japonica should be treated (again) as an independent species, T. japonica.
Collapse
Affiliation(s)
- Inkyu Park
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungyu Yang
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Sungwook Chae
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| |
Collapse
|
35
|
Scobeyeva VA, Artyushin IV, Krinitsina AA, Nikitin PA, Antipin MI, Kuptsov SV, Belenikin MS, Omelchenko DO, Logacheva MD, Konorov EA, Samoilov AE, Speranskaya AS. Gene Loss, Pseudogenization in Plastomes of Genus Allium ( Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions. Front Genet 2021; 12:674783. [PMID: 34306019 PMCID: PMC8296844 DOI: 10.3389/fgene.2021.674783] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus—Allium—is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes’ annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the “normal” or “pseudo” state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
Collapse
Affiliation(s)
- Victoria A Scobeyeva
- Department of Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasiya A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim I Antipin
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei V Kuptsov
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim S Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, Moscow, Russia
| | - Maria D Logacheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgenii A Konorov
- Laboratory of Animal Genetics, Vavilov Institute of General Genetics, Russian Academy of Science (RAS), Moscow, Russia
| | - Andrey E Samoilov
- Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna S Speranskaya
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Zhang Y, Wang Z, Guo Y, Chen S, Xu X, Wang R. Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships. Gene 2021; 791:145715. [PMID: 33984444 DOI: 10.1016/j.gene.2021.145715] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022]
Abstract
Leptodermis scabrida complex is one of the important components of genus Leptodermis, which is mainly distributed in the Himalaya Mountains. It includes species of L. gracilis, L. hirsutiflora, L. hirsutiflora var. ciliata, L. kumaonensis, L. pilosa var. acanthoclada and L. scabrida. However, species boundaries and relationships within this complex are unclear based on current morphological and molecular evidence. We sequenced 13 complete chloroplast (cp) genomes representing seven taxa of the complex and two non-Leptodermis scabrida complex taxa. After de novo assembly and annotation, we performed comparative genomic analysis. All cp genomes showed highly conserved structures, and the genome sizes ranged from 154,369 bp to 154,885 bp and possessed the same GC content (37.5%). A total of 113 unique genes were identified in each cp sample, including 79 protein coding genes, 30 tRNAs, and four rRNAs. Repeat sequences and SSRs were detected, showing great similarity among all taxa in this complex. Six highly variable regions, including trnS-trnG, rps2-rpoC2, ndhF, rpl32-ccsA, ccsA-ndhD, and ndhA, were screened as potential molecular markers for phylogenetic reconstruction. Based on a total of 27 complete cp genome sequences, the consistent and robust phylogenetic relationships were firstly constructed and the same species within L. scabrida complex clustered into a group. The divergence time of Leptodermis from ancestral taxa occurred at the middle Eocene, which might be due to geological and climatic changes. The 13 complete cp genome sequences reported will provide new clues for phylogeny elucidation, species identification and evolutionary history speculation of Leptodermis, as well as in Rubiaceae.
Collapse
Affiliation(s)
- Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengfeng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yanan Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Sheng Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianyi Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ruijiang Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
38
|
Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. BMC Genomics 2021; 22:194. [PMID: 33736599 PMCID: PMC7977240 DOI: 10.1186/s12864-021-07467-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background Lima bean (Phaseolus lunatus L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited. Results The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the P. lunatus Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae. rpl16, accD, petB, rsp16, clpP, ndhA, ndhF and ycf1 genes in coding regions was found significant variation, the intergenic regions of trnk-rbcL, rbcL-atpB, ndhJ-rps4, psbD-rpoB, atpI-atpA, atpA-accD, accD-psbJ, psbE-psbB, rsp11-rsp19, ndhF-ccsA was found in a high degree of divergence. A phylogenetic analysis showed that P. lunatus appears to be more closely related to P. vulgaris, V.unguiculata and V. radiata. Conclusions The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07467-8.
Collapse
|
39
|
Rana S, Valentin K, Riehl J, Blanfuné A, Reynes L, Thibaut T, Bartsch I, Eichinger L, Glöckner G. Analysis of organellar genomes in brown algae reveals an independent introduction of similar foreign sequences into the mitochondrial genome. Genomics 2021; 113:646-654. [PMID: 33485954 DOI: 10.1016/j.ygeno.2021.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/19/2020] [Accepted: 01/18/2021] [Indexed: 11/21/2022]
Abstract
Kelp species (Laminariales, Phaeophyceae) are globally widespread along temperate to Polar rocky coastal lines. Here we analyse the mitochondrial and chloroplast genomes of Laminaria rodriguezii, in comparison to the organellar genomes of other kelp species. We also provide the complete mitochondrial genome sequence of another endemic kelp species from a Polar habitat, the Arctic Laminaria solidungula. We compare phylogenetic trees derived from twenty complete mitochondrial and seven complete chloroplast kelp genomes. Interestingly, we found a stretch of more than 700 bp in the mitochondrial genome of L.rodriguezii, which is not present in any other yet sequenced member of the Phaeophyceae. This stretch matches a protein coding region in the mitochondrial genome from Desmarestia viridis, another brown seaweed. Their high similarity suggests that these sequences originated through independent introduction into the two species. Their origin could have been by infection by yet unknown similar mitoviruses, currently only known from fungi and plants.
Collapse
Affiliation(s)
- Shivani Rana
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Klaus Valentin
- Alfred-Wegener-Institute, Helmholtz-Center for Marine and Polar Research, Bremerhaven, Germany.
| | - Jana Riehl
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Aurélie Blanfuné
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Lauric Reynes
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Thierry Thibaut
- Aix-Marseille University and University of Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Inka Bartsch
- Alfred-Wegener-Institute, Helmholtz-Center for Marine and Polar Research, Bremerhaven, Germany
| | - Ludwig Eichinger
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany.
| | - Gernot Glöckner
- Institute of Biochemistry I, Faculty of Medicine, University of Cologne, Cologne, Germany
| |
Collapse
|
40
|
Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| |
Collapse
|
41
|
Namgung J, Do HDK, Kim C, Choi HJ, Kim JH. Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae). Sci Rep 2021; 11:3262. [PMID: 33547390 PMCID: PMC7865063 DOI: 10.1038/s41598-021-82692-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.
Collapse
Affiliation(s)
- Ju Namgung
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
| | - Hoang Dang Khoa Do
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Changkyun Kim
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea
| | - Hyeok Jae Choi
- Department of Biology and Chemistry, Changwon National University, Gyeongsangnamdo, 51140, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, 13120, Republic of Korea.
| |
Collapse
|
42
|
Khapilina O, Raiser O, Danilova A, Shevtsov V, Turzhanova A, Kalendar R. DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai. PeerJ 2021; 9:e10674. [PMID: 33510974 PMCID: PMC7798630 DOI: 10.7717/peerj.10674] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan's Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.
Collapse
Affiliation(s)
| | - Olesya Raiser
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | | | | | | | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Aqmola, Kazakhstan
| |
Collapse
|
43
|
Park I, Yang S, Song JH, Moon BC. Dissection for Floral Micromorphology and Plastid Genome of Valuable Medicinal Borages Arnebia and Lithospermum (Boraginaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:606463. [PMID: 33343605 PMCID: PMC7746654 DOI: 10.3389/fpls.2020.606463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/16/2020] [Indexed: 05/03/2023]
Abstract
The genera Arnebia and Lithospermum (Lithospermeae-Boraginaceae) comprise 25-30 and 50-60 species, respectively. Some of them are economically valuable, as their roots frequently contain a purple-red dye used in the cosmetic industry. Furthermore, dried roots of Arnebia euchroma, A. guttata, and Lithospermum erythrorhizon, which have been designated Lithospermi Radix, are used as traditional Korean herbal medicine. This study is the first report on the floral micromorphology and complete chloroplast (cp) genome sequences of A. guttata (including A. tibetana), A. euchroma, and L. erythrorhizon. We reveal great diversity in floral epidermal cell patterns, gynoecium, and structure of trichomes. The cp genomes were 149,361-150,465 bp in length, with conserved quadripartite structures. In total, 112 genes were identified, including 78 protein-coding regions, 30 tRNA genes, and four rRNA genes. Gene order, content, and orientation were highly conserved and were consistent with the general structure of angiosperm cp genomes. Comparison of the four cp genomes revealed locally divergent regions, mainly within intergenic spacer regions (atpH-atpI, petN-psbM, rbcL-psaI, ycf4-cemA, ndhF-rpl32, and ndhC-trnV-UAC). To facilitate species identification, we developed molecular markers psaA- ycf3 (PSY), trnI-CAU- ycf2 (TCY), and ndhC-trnV-UAC (NCTV) based on divergence hotspots. High-resolution phylogenetic analysis revealed clear clustering and a close relationship of Arnebia to its Lithospermum sister group, which was supported by strong bootstrap values and posterior probabilities. Overall, gynoecium characteristics and genetic distance of cp genomes suggest that A. tibetana, might be recognized as an independent species rather than a synonym of A. guttata. The present morphological and cp genomic results provide useful information for future studies, such as taxonomic, phylogenetic, and evolutionary analysis of Boraginaceae.
Collapse
Affiliation(s)
| | | | - Jun-Ho Song
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| | - Byeong Cheol Moon
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, South Korea
| |
Collapse
|
44
|
Khandagale K, Krishna R, Roylawar P, Ade AB, Benke A, Shinde B, Singh M, Gawande SJ, Rai A. Omics approaches in Allium research: Progress and way ahead. PeerJ 2020; 8:e9824. [PMID: 32974094 PMCID: PMC7486827 DOI: 10.7717/peerj.9824] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 08/05/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. METHOD In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. RESULTS Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. CONCLUSION All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.
Collapse
Affiliation(s)
- Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ram Krishna
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Praveen Roylawar
- Department of Botany, S. N. Arts, D. J. M. Commerce and B. N. S. Science College, Sangamner, India
| | - Avinash B. Ade
- Department of Botany, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Ashwini Benke
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | - Bharat Shinde
- Vidya Pratishthans’s Arts Science and commerce college, Baramati, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research, Rajgurunagar, India
| | | | - Ashutosh Rai
- Crop Improvement, ICAR-Indian Institute of Vegetable Research, Varanasi, India
| |
Collapse
|
45
|
The Role of Chloroplast Gene Expression in Plant Responses to Environmental Stress. Int J Mol Sci 2020; 21:ijms21176082. [PMID: 32846932 PMCID: PMC7503970 DOI: 10.3390/ijms21176082] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
Chloroplasts are plant organelles that carry out photosynthesis, produce various metabolites, and sense changes in the external environment. Given their endosymbiotic origin, chloroplasts have retained independent genomes and gene-expression machinery. Most genes from the prokaryotic ancestors of chloroplasts were transferred into the nucleus over the course of evolution. However, the importance of chloroplast gene expression in environmental stress responses have recently become more apparent. Here, we discuss the emerging roles of the distinct chloroplast gene expression processes in plant responses to environmental stresses. For example, the transcription and translation of psbA play an important role in high-light stress responses. A better understanding of the connection between chloroplast gene expression and environmental stress responses is crucial for breeding stress-tolerant crops better able to cope with the rapidly changing environment.
Collapse
|
46
|
Li DM, Ye YJ, Xu YC, Liu JM, Zhu GF. Complete chloroplast genomes of Zingiber montanum and Zingiber zerumbet: Genome structure, comparative and phylogenetic analyses. PLoS One 2020; 15:e0236590. [PMID: 32735595 PMCID: PMC7394419 DOI: 10.1371/journal.pone.0236590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022] Open
Abstract
Zingiber montanum (Z. montanum) and Zingiber zerumbet (Z. zerumbet) are important medicinal and ornamental herbs in the genus Zingiber and family Zingiberaceae. Chloroplast-derived markers are useful for species identification and phylogenetic studies, but further development is warranted for these two Zingiber species. In this study, we report the complete chloroplast genomes of Z. montanum and Z. zerumbet, which had lengths of 164,464 bp and 163,589 bp, respectively. These genomes had typical quadripartite structures with a large single copy (LSC, 87,856-89,161 bp), a small single copy (SSC, 15,803-15,642 bp), and a pair of inverted repeats (IRa and IRb, 29,393-30,449 bp). We identified 111 unique genes in each chloroplast genome, including 79 protein-coding genes, 28 tRNAs and 4 rRNA genes. We analyzed the molecular structures, gene information, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats (SSRs) and long repeats from the two chloroplast genomes. A comparison of the Z. montanum and Z. zerumbet chloroplast genomes detected 489 single-nucleotide polymorphisms (SNPs) and 172 insertions/deletions (indels). Thirteen highly divergent regions, including ycf1, rps19, rps18-rpl20, accD-psaI, psaC-ndhE, psbA-trnK-UUU, trnfM-CAU-rps14, trnE-UUC-trnT-UGU, ccsA-ndhD, psbC-trnS-UGA, start-psbA, petA-psbJ, and rbcL-accD, were identified and might be useful for future species identification and phylogeny in the genus Zingiber. Positive selection was observed for ATP synthase (atpA and atpB), RNA polymerase (rpoA), small subunit ribosomal protein (rps3) and other protein-coding genes (accD, clpP, ycf1, and ycf2) based on the Ka/Ks ratios. Additionally, chloroplast SNP-based phylogeny analyses found that Zingiber was a monophyletic sister branch to Kaempferia and that chloroplast SNPs could be used to identify Zingiber species. The genome resources in our study provide valuable information for the identification and phylogenetic analysis of the genus Zingiber and family Zingiberaceae.
Collapse
Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuan-Jun Ye
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ye-Chun Xu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jin-Mei Liu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| |
Collapse
|
47
|
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.
Collapse
|
48
|
Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1732586. [PMID: 32420321 PMCID: PMC7201574 DOI: 10.1155/2020/1732586] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/07/2019] [Indexed: 11/22/2022]
Abstract
Recent advances in molecular phylogenetics provide us with information of Allium L. taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species. However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved. In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species. The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp. Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content. Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered. The selection analysis showed that some genes have elevated Ka/Ks ratios. Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A. cyathophorum var. farreri was sister to A. spicatum with 100% bootstrap value. Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment. We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.
Collapse
|
49
|
The twelve blooms of Christmas. NATURE PLANTS 2019; 5:1195. [PMID: 31819226 DOI: 10.1038/s41477-019-0574-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
|