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He S, Xu B, Chen S, Li G, Zhang J, Xu J, Wu H, Li X, Yang Z. Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome. BMC Genomics 2024; 25:384. [PMID: 38637729 PMCID: PMC11027378 DOI: 10.1186/s12864-024-10278-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear. RESULTS We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species. CONCLUSIONS These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.
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Affiliation(s)
- Shuilian He
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Bin Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Siyun Chen
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China
| | - Gengyun Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Jie Zhang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Junqiang Xu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Hang Wu
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Xuejiao Li
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Zhengan Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
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Ben Romdhane W, Al-Doss A, Hassairi A. The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species. Sci Rep 2024; 14:6472. [PMID: 38499663 PMCID: PMC10948853 DOI: 10.1038/s41598-024-57141-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.
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Affiliation(s)
- Walid Ben Romdhane
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia.
| | - Abdullah Al-Doss
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Afif Hassairi
- College of Food and Agricultural Sciences, Plant Production Department, King Saud University, P.O. Box 2460, 11451, Riyadh, Saudi Arabia.
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Wang H, Zhang Y, Zhang L, Wang J, Guo H, Zong J, Chen J, Li D, Li L, Liu J, Li J. Molecular Characterization and Phylogenetic Analysis of Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence. Curr Issues Mol Biol 2024; 46:1635-1650. [PMID: 38392224 PMCID: PMC10888139 DOI: 10.3390/cimb46020106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.
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Affiliation(s)
- Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
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Lubna, Asaf S, Jan R, Asif S, Bilal S, Khan AL, Al-Rawahi AN, Kim KM, Al-Harrasi A. The complete plastome sequences of invasive weed Parthenium hysterophorus: genome organization, evolutionary significance, structural features, and comparative analysis. Sci Rep 2024; 14:4006. [PMID: 38369569 PMCID: PMC10874969 DOI: 10.1038/s41598-024-54503-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Parthenium hysterophorus, a globally widespread weed, poses a significant threat to agricultural ecosystems due to its invasive nature. We investigated the chloroplast genome of P. hysterophorus in this study. Our analysis revealed that the chloroplast genome of P. hysterophorus spans a length of 151,881 base pairs (bp). It exhibits typical quadripartite structure commonly found in chloroplast genomes, including inverted repeat regions (IR) of 25,085 bp, a small single copy (SSC) region of 18,052 bp, and a large single copy (LSC) region of 83,588 bp. A total of 129 unique genes were identified in P. hysterophorus chloroplast genomes, including 85 protein-coding genes, 36 tRNAs, and eight rRNAs genes. Comparative analysis of the P. hysterophorus plastome with those of related species from the tribe Heliantheae revealed both conserved structures and intriguing variations. While many structural elements were shared among the species, we identified a rearrangement in the large single-copy region of P. hysterophorus. Moreover, our study highlighted notable gene divergence in several specific genes, namely matK, ndhF, clpP, rps16, ndhA, rps3, and ndhD. Phylogenetic analysis based on the 72 shared genes placed P. hysterophorus in a distinct clade alongside another species, P. argentatum. Additionally, the estimated divergence time between the Parthenium genus and Helianthus (sunflowers) was approximately 15.1 million years ago (Mya). These findings provide valuable insights into the evolutionary history and genetic relationships of P. hysterophorus, shedding light on its divergence and adaptation over time.
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Affiliation(s)
- Lubna
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Rahmatullah Jan
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saleem Asif
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Saqib Bilal
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Sugar Land, TX, 77479, USA
| | - Ahmed N Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Kyung-Min Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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Caycho E, La Torre R, Orjeda G. Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae). BMC Plant Biol 2023; 23:570. [PMID: 37974117 PMCID: PMC10652460 DOI: 10.1186/s12870-023-04581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.
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Affiliation(s)
- Esteban Caycho
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Renato La Torre
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru
| | - Gisella Orjeda
- Laboratory of Genomics and Bioinformatics for Biodiversity, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, 15081, Lima, Peru.
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An SM, Kim BY, Kang H, Lee HR, Lee YB, Park YJ, Cheon KS, Kim KA. The complete chloroplast genome sequences of six Hylotelephium species: Comparative genomic analysis and phylogenetic relationships. PLoS One 2023; 18:e0292056. [PMID: 37815995 PMCID: PMC10564136 DOI: 10.1371/journal.pone.0292056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
To evaluate the phylogenetic relationships between Hylotelephium and Orostachys, and to provide important information for further studies, we analyzed the complete chloroplast genomes of six Hylotelephium species and compared the sequences to those of published chloroplast genomes of congeneric species and species of the closely related genus, Orostachys. The total chloroplast genome length of nineteen species, including the six Hylotelephium species analyzed in this study and the thirteen Hylotelephium and Orostachys species analyzed in previous studies, ranged from 150,369 bp (O. minuta) to 151,739 bp (H. spectabile). Their overall GC contents were almost identical (37.7-37.8%). The chloroplast genomes of the nineteen species contained 113 unique genes comprising 79 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Among the annotated genes, fourteen genes contained one intron, and two genes contained two introns. The chloroplast genomes of the nineteen Hylotelephium and Orostachys species had identical structures. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved in the Hylotelephium and Orostachys species. The nucleotide diversity between the Hylotelephium chloroplast genomes was extremely low in all regions, and only one region showed a high Pi value (>0.03). In all nineteen chloroplast genomes, six regions had a high Pi value (>0.03). The phylogenetic analysis showed that the genus delimitation could not be clearly observed even in this study because Hylotelephium formed a paraphyly with subsect. Orostachys of the genus Orostachys. Additionally, the data supported the taxonomic position of Sedum taqeutii, which was treated as a synonym for H. viridescens in previous studies, as an independent taxon.
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Affiliation(s)
- Sung-Mo An
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Halam Kang
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Ha-Rim Lee
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Yoo-Bin Lee
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Yoo-Jung Park
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Kyeong-Sik Cheon
- Department of Biological Science, Sangji University, Wonju, South Korea
| | - Kyung-Ah Kim
- Environmental Research Institute, Kangwon National University, Chuncheon, South Korea
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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Li Y, Hu X, Xiao M, Huang J, Lou Y, Hu F, Fu X, Li Y, He H, Cheng J. An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea. BMC Genom Data 2023; 24:42. [PMID: 37558997 PMCID: PMC10413492 DOI: 10.1186/s12863-023-01143-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. RESULTS Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. CONCLUSION This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.
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Affiliation(s)
- Yaqi Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Xiang Hu
- Institute of Tropical Eco-Agricultural, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan, China
| | - Mingkun Xiao
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Jiaxiong Huang
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yuqiang Lou
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Faguang Hu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Xingfei Fu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Hongyan He
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
- Yunnan Academy of Agricultural Engineering, Kunming, Yunnan, China
| | - Jinhuan Cheng
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China.
- Yunnan Academy of Agricultural Engineering, Kunming, Yunnan, China.
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Yuan S, Nie C, Jia S, Liu T, Zhao J, Peng J, Kong W, Liu W, Gou W, Lei X, Xiong Y, Xiong Y, Yu Q, Ling Y, Ma X. Complete chloroplast genomes of three wild perennial Hordeum species from Central Asia: genome structure, mutation hotspot, phylogenetic relationships, and comparative analysis. Front Plant Sci 2023; 14:1170004. [PMID: 37554563 PMCID: PMC10405828 DOI: 10.3389/fpls.2023.1170004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
Hordeum L. is widely distributed in mountain or plateau of subtropical and warm temperate regions around the world. Three wild perennial Hordeum species, including H. bogdanii, H. brevisubulatum, and H. violaceum, have been used as forage and for grassland ecological restoration in high-altitude areas in recent years. To date, the degree of interspecies sequence variation in the three Hordeum species within existing gene pools is still not well-defined. Herein, we sequenced and assembled chloroplast (cp) genomes of the three species. The results revealed that the cp genome of H. bogdanii showed certain sequence variations compared with the cp genomes of the other two species (H. brevisubulatum and H. violaceum), and the latter two were characterized by a higher relative affinity. Parity rule 2 plot (PR2) analysis illuminated that most genes of all ten Hordeum species were concentrated in nucleotide T and G. Numerous single nucleotide polymorphism (SNP) and insertion/deletion (In/Del) events were detected in the three Hordeum species. A series of hotspots regions (tRNA-GGU ~ tRNA-GCA, tRNA-UGU ~ ndhJ, psbE ~ rps18, ndhF ~ tRNA-UAG, etc.) were identified by mVISTA procedures, and the five highly polymorphic genes (tRNA-UGC, tRNA-UAA, tRNA-UUU, tRNA-UAC, and ndhA) were proved by the nucleotide diversity (Pi). Although the distribution and existence of cp simple sequence repeats (cpSSRs) were predicted in the three Hordeum cp genomes, no rearrangement was found between them. A similar phenomenon has been found in the cp genome of the other seven Hordeum species, which has been published so far. In addition, evolutionary relationships were reappraised based on the currently reported cp genome of Hordeum L. This study offers a framework for gaining a better understanding of the evolutionary history of Hordeum species through the re-examination of their cp genomes, and by identifying highly polymorphic genes and hotspot regions that could provide important insights into the genetic diversity and differentiation of these species.
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Affiliation(s)
- Shuai Yuan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Cong Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Tianqi Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinghan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Weixia Kong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yao Ling
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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Hu K, Sun XQ, Chen M, Lu RS. Low-coverage whole genome sequencing of eleven species/subspecies in Dioscorea sect. Stenophora (Dioscoreaceae): comparative plastome analyses, molecular markers development and phylogenetic inference. Front Plant Sci 2023; 14:1196176. [PMID: 37346115 PMCID: PMC10281252 DOI: 10.3389/fpls.2023.1196176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/26/2023] [Indexed: 06/23/2023]
Abstract
Dioscorea sect. Stenophora (Dioscoreaceae) comprises about 30 species that are distributed in the temperate and subtropical regions of the Northern Hemisphere. Despite being evolutionarily "primitive" and medically valuable, genomic resources and molecular studies of this section are still scarce. Here, we conducted low-coverage whole genome sequencing of 11 Stenophora species/subspecies to retrieve their plastome information (whole plastome characteristics, plastome-divergent hotspots, plastome-derived SSRs, etc.) and polymorphic nuclear SSRs, as well as performed comparative plastome and phylogenetic analyses within this section. The plastomes of Stenophora species/subspecies ranged from 153,691 bp (D. zingiberensis) to 154,149 bp (D. biformifolia) in length, and they all contained the same 114 unique genes. All these plastomes were highly conserved in gene structure, gene order and GC content, although variations at the IR/SC borders contributed to the whole length differences among them. The number of plastome-derived SSRs among Stenophora species/subspecies varied from 74 (D. futschauensis) to 93 (D. zingiberensis), with A/T found to be the most frequent one. Seven highly variable regions and 12 polymorphic nuclear SSRs were identified in this section, thereby providing important information for further taxonomical, phylogenetic and population genetic studies. Phylogenomic analyses based on whole plastome sequences and 80 common protein coding genes strongly supported D. biformifolia and D. banzhuana constituted the successive sister species to the remaining sampled species, which could be furtherly divided into three clades. Overall, this study provided a new perspective for plastome evolution of Stenophora, and proved the role of plastome phylogenomic in improving the phylogenetic resolution in this section. These results also provided an important reference for the protection and utilization of this economically important section.
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Affiliation(s)
- Ke Hu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
| | - Rui-Sen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia).
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Affiliation(s)
- Rana M Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Hassan Mansour
- Department of Biological Sciences, Faculty of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Shouaa A Alrobaish
- Department of Biology, College of Science, Qassim University, Buraydah 52377, Saudi Arabia
| | - Najla A Al Shaye
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
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AbdAlla HAM, Wanga VO, Mkala EM, Amenu SG, Amar MH, Chen L, Wang QF. Comparative genomics analysis of endangered wild Egyptian Moringa peregrina (Forssk.) Fiori plastome, with implications for the evolution of Brassicales order. Front Genet 2023; 14:1131644. [PMID: 36992699 PMCID: PMC10040795 DOI: 10.3389/fgene.2023.1131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Moringa is a mono-genus belonging to the Moringaceae family, which includes 13 species. Among them, Moringa peregrina is plant species native to the Arabian Peninsula, Southern Sinai in Egypt, and the Horn of Africa, and comprehensive studies on its nutritional, industrial, and medicinal values have been performed. Herein, we sequenced and analyzed the initial complete chloroplast genome of Moringa peregrina. Concurrently, we analyzed the new chloroplast genome along with 25 chloroplast genomes related to species representing eight families in the Brassicales order. The results indicate that the plastome sequence of M. peregrina consists of 131 genes, with an average GC content of 39.23%. There is a disparity in the IR regions of the 26 species ranging from 25,804 to 31,477 bp. Plastome structural variations generated 20 hotspot regions that could be considered prospective DNA barcode locations in the Brassicales order. Tandem repeats and SSR structures are reported as significant evidence of structural variations among the 26 tested specimens. Furthermore, selective pressure analysis was performed to estimate the substitution rate within the Moringaceae family, which revealing that the ndhA and accD genes are under positive selective pressure. The phylogenetic analysis of the Brassicales order produced an accurate monophyletic annotation cluster of the Moringaceae and Capparaceae species, offering unambiguous identification without overlapping groups between M. oleifera and M. peregrina, which are genetically strongly associated. Divergence time estimation suggests that the two Moringa species recently diversified, 0.467 Ma. Our findings highlight the first complete plastome of the Egyptian wild-type of M. peregrina, which can be used for determining plastome phylogenetic relationships and systematic evolution history within studies on the Moringaceae family.
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Affiliation(s)
- Heba A. M. AbdAlla
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Botany Department, Agriculture and Biological Institute, National Research Centre, Giza, Egypt
| | - Vincent Okelo Wanga
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Sara Getachew Amenu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
| | - Mohamed Hamdy Amar
- Egyptian Deserts Gene Bank, Desert Research Center, Cairo, Egypt
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Lingyun Chen
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Plant Biodiversity and Evolution Research Group, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Qing-Feng Wang, ; Lingyun Chen, ; Mohamed Hamdy Amar,
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Kuang Q, Sheng W. The entire chloroplast genome sequence of Asparagus setaceus (Kunth) Jessop: Genome structure, gene composition, and phylogenetic analysis in Asparagaceae. Open Life Sci 2022; 17:1541-1554. [DOI: 10.1515/biol-2022-0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/24/2022] Open
Abstract
Abstract
Asparagus setaceus (Kunth) Jessop is a horticultural plant of the genus Asparagus. Herein, the whole chloroplast (cp) genome of A. setaceus was sequenced with PacBio and Illumina sequencing systems. The cp genome shows a characteristic quadripartite structure with 158,076 bp. In total, 135 genes were annotated, containing 89 protein-coding, 38 tRNA, and 8 rRNA genes. Contrast with the previous cp genome of A. setaceus registered in NCBI, we identified 7 single-nucleotide polymorphisms and 15 indels, mostly situated in noncoding areas. Meanwhile, 36 repeat structures and 260 simple sequence repeats were marked out. A bias for A/T-ending codons was shown in this cp genome. Furthermore, we predicted 78 RNA-editing sites in 29 genes, which were all for C-to-U transitions. And it was also proven that positive selection was exerted on the rpoC1 gene of A. setaceus with the K
a/K
s data. Meanwhile, a conservative gene order and highly similar sequences of protein-coding genes were revealed within Asparagus species. Phylogenetic tree analysis indicated that A. setaceus was a sister to Asparagus cochinchinensis. Taken together, our released genome provided valuable information for the gene composition, genetics comparison, and the phylogeny studies of A. setaceus.
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Affiliation(s)
- Quan Kuang
- Department of Biological Technology, Nanchang Normal University , Nanchang , 330032, Jiangxi , China
| | - Wentao Sheng
- Department of Biological Technology, Nanchang Normal University , Nanchang , 330032, Jiangxi , China
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14
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Lin P, Yin H, Wang K, Gao H, Liu L, Yao X. Comparative Genomic Analysis Uncovers the Chloroplast Genome Variation and Phylogenetic Relationships of Camellia Species. Biomolecules 2022; 12:biom12101474. [PMID: 36291685 PMCID: PMC9599789 DOI: 10.3390/biom12101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Camellia is the largest genus in the family Theaceae. Due to phenotypic diversity, frequent hybridization, and polyploidization, an understanding of the phylogenetic relationships between Camellia species remains challenging. Comparative chloroplast (cp) genomics provides an informative resource for phylogenetic analyses of Camellia. In this study, 12 chloroplast genome sequences from nine Camellia species were determined using Illumina sequencing technology via de novo assembly. The cp genome sizes ranged from 156,545 to 157,021 bp and were organized into quadripartite regions with the typical angiosperm cp genomes. Each genome harbored 87 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes in the same order and orientation. Differences in long and short sequence repeats, SNPs, and InDels were detected across the 12 cp genomes. Combining with the complete cp sequences of seven other species in the genus Camellia, a total of nine intergenic sequence divergent hotspots and 14 protein-coding genes with high sequence polymorphism were identified. These hotspots, especially the InDel (~400 bp) located in atpH-atpI region, had sufficient potential to be used as barcode markers for further phylogenetic analysis and species identification. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These cp genomes could facilitate the development of new molecular markers, accurate species identification, and investigations of the phylogenomic relationships of the genus Camellia.
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Affiliation(s)
- Ping Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Correspondence: (P.L.); (X.Y.); Tel.: +86-571-63320229 (P.L.)
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Haidong Gao
- Genepioneer Biotechnologies Co., Ltd., Nanjing 210023, China
| | - Lei Liu
- Genepioneer Biotechnologies Co., Ltd., Nanjing 210023, China
| | - Xiaohua Yao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Key Laboratory of Tree Breeding of Zhejiang Province, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
- Correspondence: (P.L.); (X.Y.); Tel.: +86-571-63320229 (P.L.)
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Fan ZF, Ma CL. Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora. Sci Rep 2022; 12:15984. [PMID: 36163343 PMCID: PMC9512918 DOI: 10.1038/s41598-022-16290-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.
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Affiliation(s)
- Zhi-Feng Fan
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.,Kunming University of Science and Technology, Kunming, 650500, People's Republic of China
| | - Chang-Le Ma
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.
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Tayşi N, Kaymaz Y, Ateş D, Sari H, Toker C, Tanyolaç MB. Complete chloroplast genome sequence of Lens ervoides and comparison to Lens culinaris. Sci Rep 2022; 12:15068. [PMID: 36064865 PMCID: PMC9445179 DOI: 10.1038/s41598-022-17877-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/02/2022] [Indexed: 12/05/2022] Open
Abstract
Lens is a member of the Papilionoideae subfamily of Fabaceae and is generally used as a source of vegetable protein as part of human diets in many regions worldwide. Chloroplast (cp) genomes are highly active genetic components of plants and can be utilized as molecular markers for various purposes. As one of the wild lentil species, the Lens ervoides cp genome has been sequenced for the first time in this study using next-generation sequencing. The de novo assembly of the cp genome resulted in a single 122,722 bp sequence as two separate coexisting structural haplotypes with similar lengths. Results indicated that the cp genome of L. ervoides belongs to the inverted repeat lacking clade. Several noteworthy divergences within the coding regions were observed in ndhB, ndhF, rbcL, rpoC2, and ycf2 genes. Analysis of relative synonymous codon usage showed that certain genes, psbN, psaI, psbI, psbE, psbK, petD, and ndhC, preferred using biased codons more often and therefore might have elevated expression and translation efficiencies. Overall, this study exhibited the divergence level between the wild-type and cultured lentil cp genomes and pointed to certain regions that can be utilized as distinction markers for various goals.
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Affiliation(s)
- Nurbanu Tayşi
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey
| | - M Bahattin Tanyolaç
- Bioengineering Department, Faculty of Engineering, Ege University, Izmir, Turkey.
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17
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Rehman O, Uzair M, Chao H, Khan MR, Chen M. Decoding RNA Editing Sites Through Transcriptome Analysis in Rice Under Alkaline Stress. Front Plant Sci 2022; 13:892729. [PMID: 35812946 PMCID: PMC9260663 DOI: 10.3389/fpls.2022.892729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleic acid editing (RE) is a post-transcriptional process that altered the genetics of RNA which provide the extra level of gene expression through insertion, deletions, and substitutions. In animals, it converts nucleotide residues C-U. Similarly in plants, the role of RNA editing sites (RES) in rice under alkaline stress is not fully studied. Rice is a staple food for most of the world population. Alkaline stress cause reduction in yield. Here, we explored the effect of alkaline stress on RES in the whole mRNA from rice chloroplast and mitochondria. Ribonucleic acid editing sites in both genomes (3336 RESs) including chloroplast (345 RESs) and mitochondria (2991 RESs) with average RES efficiency ∼55% were predicted. Our findings showed that majority of editing events found in non-synonymous codon changes and change trend in amino acids was hydrophobic. Four types of RNA editing A-G (A-I), C-T (C-U), G-A, and T-C were identified in treated and untreated samples. Overall, RNA editing efficiency was increased in the treated samples. Analysis of Gene Ontology revealed that mapped genes were engaged in many biological functions and molecular processes. We also checked the expression of pentatricopeptide repeat (PPR), organelle zinc-finger (OZI), and multiple organellar RNA editing factors/RNA editing factor interacting proteins genes in control and treatment, results revealed upregulation of PPR and OZ1 genes in treated samples. This induction showed the role of these genes in RNA editing. The current findings report that RNA editing increased under alkaline stress which may contribute in adaptation for rice by changing amino acids in edited genes (88 genes). These findings will provide basis for identification of RES in other crops and also will be useful in alkaline tolerance development in rice.
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Affiliation(s)
- Obaid Rehman
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
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Wong K, Wu H, Kong BL, But GW, Siu T, Hui JH, Shaw P, Lau DT. Characterisation of the Complete Chloroplast Genomes of Seven Hyacinthus orientalis L. Cultivars: Insights into Cultivar Phylogeny. Horticulturae 2022; 8:453. [DOI: 10.3390/horticulturae8050453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To improve agricultural performance and obtain potential economic benefits, an understanding of phylogenetic relationships of Hyacinthus cultivars is needed. This study aims to revisit the phylogenetic relationships of Hyacinthus cultivars using complete chloroplast genomes. Nine chloroplast genomes were de novo sequenced, assembled and annotated from seven cultivars of Hyacinthus orientalis and two Scilloideae species including Bellevalia paradoxa and Scilla siberica. The chloroplast genomes of Hyacinthus cultivars ranged from 154,458 bp to 154,641 bp, while those of Bellevalia paradoxa and Scilla siberica were 154,020 bp and 154,943 bp, respectively. Each chloroplast genome was annotated with 133 genes, including 87 protein-coding genes, 38 transfer RNA genes and 8 ribosomal RNA genes. Simple sequence repeats AAGC/CTTG and ACTAT/AGTAT were identified only in ‘Eros’, while AAATC/ATTTG were identified in all cultivars except ‘Eros’. Five haplotypes were identified based on 460 variable sites. Combined with six other previously published chloroplast genomes of Scilloideae, a sliding window analysis and a phylogenetic analysis were performed. Divergence hotspots ndhA and trnG-UGC were identified with a nucleotide diversity threshold at 0.04. The phylogenetic positions of Hyacinthus cultivars were different from the previous study using ISSR. Complete chloroplast genomes serve as new evidence in Hyacinthus cultivar phylogeny, contributing to cultivar identification, preservation and breeding.
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Ren T, Aou X, Tian R, Li Z, Peng C, He X. Complete Chloroplast Genome of Cnidium monnieri (Apiaceae) and Comparisons with Other Tribe Selineae Species. Diversity 2022; 14:323. [DOI: 10.3390/d14050323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cnidium monnieri is an economically important traditional Chinese medicinal plant. In this study, the complete chloroplast (cp) genome of C. monnieri was determined using the Illumina paired-end sequencing, the GetOrganelle de novo assembly strategy, as well as the GeSeq annotation method. Our results showed that the cp genome was 147,371 bp in length with 37.4% GC content and included a large single-copy region (94,361 bp) and a small single-copy region (17,552 bp) separated by a pair of inverted repeat regions (17,729 bp). A total of 129 genes were contained in the cp genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. We also investigated codon usage, RNA editing, repeat sequences, simple sequence repeats (SSRs), IR boundaries, and pairwise Ka/Ks ratios. Four hypervariable regions (trnD-trnY-trnE-trnT, ycf2, ndhF-rpl32-trnL, and ycf1) were identified as candidate molecular markers for species authentication. The phylogenetic analyses supported non-monophyly of Cnidium and C. monnieri located in tribe Selineae based on the cp genome sequences and internal transcribed spacer (ITS) sequences. The incongruence of the phylogenetic position of C. monnieri between ITS and cpDNA phylogenies suggested that C. monnieri might have experienced complex evolutions with hybrid and incomplete lineage sorting. All in all, the results presented herein will provide plentiful chloroplast genomic resources for studies of the taxonomy, phylogeny, and species authentication of C. monnieri. Our study is also conducive to elucidating the phylogenetic relationships and taxonomic position of Cnidium.
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Zhang G, Wang H, Shi L, Liu Y, Yao R, Sui C, Yang C, Ji H, Wang Q, Wei J. Identification of the original plants of cultivated Bupleuri Radix based on DNA barcoding and chloroplast genome analysis. PeerJ 2022; 10:e13208. [PMID: 35433122 PMCID: PMC9012172 DOI: 10.7717/peerj.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/10/2022] [Indexed: 01/12/2023] Open
Abstract
Bupleuri Radix is the dry root of certain species of the genus Bupleurum and is commonly used in traditional Chinese medicine. The increasing global demand for Bupleuri Radix cannot be fulfilled with wild populations only. Therefore, cultivated Bupleurum is now the main commercial source of this medicinal product. Different species of Bupleurum show different medicinal properties and clinical effects, making reliable authentication and assignment of correct botanical origin for medicinal species critical. However, accurate identification of the cultivated Bupleurum species is difficult due to dramatic morphological variations resulting from cultivation. In this study, we sampled 56 cultivated Bupleurum populations of six different morphotypes (Types A-F) from the main production areas of China, and 10 wild populations of four species were used as reference materials. Conventional DNA barcoding was conducted to identify cultivated Bupleurum species. Additionally, verification based on complete chloroplast genomes was performed and new chloroplast markers were developed and evaluated. The combination of these methods resulted in the successful identification of all cultivated Bupleurum individuals. Three chloroplast regions are recommended as additional barcodes for the genus: ycf4_cemA, psaJ_rpl33, and ndhE_ndhG. This is a reliable and promising strategy that can be applied to the authentication of natural products and the identification of other medicinal plant species with similar taxonomic problems.
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Affiliation(s)
- Gaixia Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China,Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruyu Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chun Sui
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengmin Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongliang Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Lubna, Asaf S, Jan R, Khan AL, Ahmad W, Asif S, Al-Harrasi A, Kim KM, Lee IJ. The Plastome Sequences of Triticum sphaerococcum (ABD) and Triticum turgidum subsp. durum (AB) Exhibit Evolutionary Changes, Structural Characterization, Comparative Analysis, Phylogenomics and Time Divergence. Int J Mol Sci 2022; 23:2783. [PMID: 35269924 DOI: 10.3390/ijms23052783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
The mechanism and course of Triticum plastome evolution is currently unknown; thus, it remains unclear how Triticum plastomes evolved during recent polyploidization. Here, we report the complete plastomes of two polyploid wheat species, Triticum sphaerococcum (AABBDD) and Triticum turgidum subsp. durum (AABB), and compare them with 19 available and complete Triticum plastomes to create the first map of genomic structural variation. Both T. sphaerococcum and T. turgidum subsp. durum plastomes were found to have a quadripartite structure, with plastome lengths of 134,531 bp and 134,015 bp, respectively. Furthermore, diploid (AA), tetraploid (AB, AG) and hexaploid (ABD, AGAm) Triticum species plastomes displayed a conserved gene content and commonly harbored an identical set of annotated unique genes. Overall, there was a positive correlation between the number of repeats and plastome size. In all plastomes, the number of tandem repeats was higher than the number of palindromic and forward repeats. We constructed a Triticum phylogeny based on the complete plastomes and 42 shared genes from 71 plastomes. We estimated the divergence of Hordeum vulgare from wheat around 11.04-11.9 million years ago (mya) using a well-resolved plastome tree. Similarly, Sitopsis species diverged 2.8-2.9 mya before Triticum urartu (AA) and Triticum monococcum (AA). Aegilops speltoides was shown to be the maternal donor of polyploid wheat genomes and diverged ~0.2-0.9 mya. The phylogeny and divergence time estimates presented here can act as a reference framework for future studies of Triticum evolution.
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Song W, Ji C, Chen Z, Cai H, Wu X, Shi C, Wang S. Comparative Analysis the Complete Chloroplast Genomes of Nine Musa Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Front Plant Sci 2022; 13:832884. [PMID: 35222490 PMCID: PMC8866658 DOI: 10.3389/fpls.2022.832884] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 06/12/2023]
Abstract
Musa (family Musaceae) is monocotyledonous plants in order Zingiberales, which grows in tropical and subtropical regions. It is one of the most important tropical fruit trees in the world. Herein, we used next-generation sequencing technology to assemble and perform in-depth analysis of the chloroplast genome of nine new Musa plants for the first time, including genome structure, GC content, repeat structure, codon usage, nucleotide diversity and etc. The entire length of the Musa chloroplast genome ranged from 167,975 to 172,653 bp, including 113 distinct genes comprising 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. In comparative analysis, we found that the contraction and expansion of the inverted repeat (IR) regions resulted in the doubling of the rps19 gene. The several non-coding sites (psbI-atpA, atpH-atpI, rpoB-petN, psbM-psbD, ndhf-rpl32, and ndhG-ndhI) and three genes (ycf1, ycf2, and accD) showed significant variation, indicating that they have the potential of molecular markers. Phylogenetic analysis based on the complete chloroplast genome and coding sequences of 77 protein-coding genes confirmed that Musa can be mainly divided into two groups. These genomic sequences provide molecular foundation for the development and utilization of Musa plants resources. This result may contribute to the understanding of the evolution pattern, phylogenetic relationships as well as classification of Musa plants.
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Affiliation(s)
- Weicai Song
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chuxuan Ji
- Department of Life Sciences, Imperial College London, Silwood Park, London, United Kingdom
| | - Zimeng Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Haohong Cai
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Xiaomeng Wu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Chao Shi
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shuo Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, China
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Asaf S, Ahmad W, Al-Harrasi A, Khan AL. Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae). BMC Genomics 2022; 23:83. [PMID: 35086490 PMCID: PMC8796432 DOI: 10.1186/s12864-022-08320-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species. RESULTS The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae. CONCLUSION All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman
| | - Waqar Ahmad
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa, 616, Nizwa, Oman.
| | - Abdul Latif Khan
- Department of Engineering Technology, University of Houston, Houston, TX, 77479, USA.
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García-valencia LE, Pérez-garcía J, Vallejo-reyna MÁ, Reynoso-santos R, Vargas-hernández J, García-campusano F. cpSSR and High-Resolution Melting Analysis (HRM) for Pinus pseudostrobus Lindl. Variety Genotyping and Discrimination. Forests 2022; 13:200. [DOI: 10.3390/f13020200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The unambiguous identification of varieties within the Pseudostrobus complex is a key step to facilitate tree selection and monitoring in the wild as well as in plantations. Molecular tools provide a powerful approach for species delimitation; however, the use of DNA barcodes in this group has met limited success due to widespread haplotype sharing from lineage sorting, hybridization and introgression. Here, we evaluate the utility of real-time PCR coupled with high-resolution melting (HRM) to discriminate among Pinus pseudostrobus Lindl. var. pseudostrobus, apulcensis and oaxacana, from wild populations in central and southern Mexico, using chloroplast DNA sequence variants located within the clpP, ycf2, trnL(UAA)–trnT(UGU) and trnI(CAU)–trnF(GAA) loci. The markers ycf2/trnL(UAA)–trnT(UGU) produced clear melting patterns that separated the varieties pseudostrobus and oaxacana from type var. apulcensis, whereas clpP discriminated over 60% of var. oaxacana individuals. This assay underlines the usefulness of these less-used DNA regions as potential biological markers and exhibits the effect of geography on allele distribution and the likely presence of hybrids among the species and varieties.
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She H, Liu Z, Xu Z, Zhang H, Cheng F, Wu J, Wang X, Qian W. Comparative chloroplast genome analyses of cultivated spinach and two wild progenitors shed light on the phylogenetic relationships and variation. Sci Rep 2022; 12:856. [PMID: 35039603 DOI: 10.1038/s41598-022-04918-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/31/2021] [Indexed: 01/30/2023] Open
Abstract
Spinacia is a genus of important leafy vegetable crops worldwide and includes cultivated Spinacia oleracea and two wild progenitors, Spinacia turkestanica and Spinacia tetrandra. However, the chloroplast genomes of the two wild progenitors remain unpublished, limiting our knowledge of chloroplast genome evolution among these three Spinacia species. Here, we reported the complete chloroplast genomes of S. oleracea, S. turkestanica, and S. tetrandra obtained via Illumina sequencing. The three chloroplast genomes exhibited a typical quadripartite structure and were 150,739, 150,747, and 150,680 bp in size, respectively. Only three variants were identified between S. oleracea and S. turkestanica, whereas 690 variants were obtained between S. oleracea and S. tetrandra, strongly demonstrating the close relationship between S. turkestanica and S. oleracea. This was further supported by phylogenetic analysis. We reported a comprehensive variant dataset including 503 SNPs and 83 Indels using 85 Spinacia accessions containing 61 S. oleracea, 16 S. turkestanica, and eight S. tetrandra accessions. Thirteen S. oleracea accessions were derived through introgression from S. turkestanica that acts as the maternal parent. Together, these results provide a valuable resource for spinach breeding programs and improve our understanding of the phylogenetic relationships within Amaranthaceae.
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Tian X, Shi L, Guo J, Fu L, Du P, Huang B, Wu Y, Zhang X, Wang Z. Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts. Front Plant Sci 2021; 12:804568. [PMID: 34975994 PMCID: PMC8718879 DOI: 10.3389/fpls.2021.804568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.
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Affiliation(s)
- Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Pei Du
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Bingyan Huang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinyou Zhang
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Henan Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Hu G, Wang Y, Wang Y, Zheng S, Dong W, Dong N. New Insight into the Phylogeny and Taxonomy of Cultivated and Related Species of Crataegus in China, Based on Complete Chloroplast Genome Sequencing. Horticulturae 2021; 7:301. [DOI: 10.3390/horticulturae7090301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hawthorns (Crataegus L.) are one of the most important processing and table fruits in China, due to their medicinal properties and health benefits. However, the interspecific relationships and evolution history of cultivated Crataegus in China remain unclear. Our previously published data showed C. bretschneideri may be derived from the hybridization of C. pinnatifida with C. maximowiczii, and that introgression occurs between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. In the present study, chloroplast sequences were used to further elucidate the phylogenetic relationships of cultivated Crataegus native to China. The chloroplast genomes of three cultivated species and one related species of Crataegus were sequenced for comparative and phylogenetic analyses. The four chloroplast genomes of Crataegus exhibited typical quadripartite structures and ranged from 159,607 bp (C. bretschneideri) to 159,875 bp (C. maximowiczii) in length. The plastomes of the four species contained 113 genes consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Six hypervariable regions (ndhC-trnV(UAC)-trnM(CAU), ndhA, atpH-atpI, ndhF, trnR(UCU)-atpA, and ndhF-rpl32), 196 repeats, and a total of 386 simple sequence repeats were detected as potential variability makers for species identification and population genetic studies. In the phylogenomic analyses, we also compared the entire chloroplast genomes of three published Crataegus species: C. hupehensis (MW201730.1), C. pinnatifida (MN102356.1), and C. marshallii (MK920293.1). Our phylogenetic analyses grouped the seven Crataegus taxa into two main clusters. One cluster included C. bretschneideri, C. maximowiczii, and C. marshallii, whereas the other included C. hupehensis, C. pinnatifida, and C. pinnatifida var. major. Taken together, our findings indicate that C. maximowiczii is the maternal origin of C. bretschneideri. This work provides further evidence of introgression between C. hupehensis, C. pinnatifida, and C. pinnatifida var. major, and suggests that C. pinnatifida var. major might have been artificially selected and domesticated from hybrid populations, rather than evolved from C. pinnatifida.
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Khan AL, Asaf S, Lubna, Al-Rawahi A, Al-Harrasi A. Decoding first complete chloroplast genome of toothbrush tree (Salvadora persica L.): insight into genome evolution, sequence divergence and phylogenetic relationship within Brassicales. BMC Genomics 2021; 22:312. [PMID: 33926374 PMCID: PMC8086069 DOI: 10.1186/s12864-021-07626-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salvadora persica L. (Toothbrush tree - Miswak; family-Salvadoraceae) grows in the arid-land ecosystem and possesses economic and medicinal importance. The species, genus and the family have no genomic datasets available specifically on chloroplast (cp) genomics and taxonomic evolution. Herein, we have sequenced the complete chloroplast genome of S. persica for the first time and compared it with 11 related specie's cp genomes from the order Brassicales. RESULTS The S. persica cp genome was 153,379 bp in length containing a sizeable single-copy region (LSC) of 83,818 bp which separated from the small single-copy region (SSC) of 17,683 bp by two inverted repeats (IRs) each 25,939 bp. Among these genomes, the largest cp genome size (160,600 bp) was found in M. oleifera, while in S. persica it was the smallest (153,379 bp). The cp genome of S. persica encoded 131 genes, including 37 tRNA genes, eight rRNA genes and 86 protein-coding genes. Besides, S. persica contains 27 forward, 36 tandem and 19 palindromic repeats. The S. persica cp genome had 154 SSRs with the highest number in the LSC region. Complete cp genome comparisons showed an overall high degree of sequence resemblance between S. persica and related cp genomes. Some divergence was observed in the intergenic spaces of other species. Phylogenomic analyses of 60 shared genes indicated that S. persica formed a single clade with A. tetracantha with high bootstrap values. The family Salvadoraceae is closely related to Capparaceae and Petadiplandraceae rather than to Bataceae and Koberliniacaea. CONCLUSION The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, genome evolution and future genetic diversity-related studies of S. persica in complex angiosperm families.
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Affiliation(s)
- Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, 616, Nizwa, Oman.
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29
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Zhang G, Kong W, Wang Q, Lu F, Jin Y, Jiang J, Shi L. A The complete chloroplast genome and phylogenetic analysis of Bupleurum yinchowense Shan & Yin Li. Mitochondrial DNA B Resour 2021; 6:1233-1235. [PMID: 33855176 PMCID: PMC8018508 DOI: 10.1080/23802359.2020.1866465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Bupleurum yinchowense Shan & Yin Li was first described as a new Bupleurum species in 1974, but its classification status has always been disputed. Here, its complete chloroplast genome was provided to resolve this issue. The length of the B. yinchowense chloroplast genome is 155,851 bp and composed of two inverted repeats (IR: 26,307 bp), a large single-copy region (LSC: 85,625 bp), and a small single-copy region (SSC: 17,612 bp). The overall GC content is 37.6%. The chloroplast genome consists of 113 genes, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Phylogenetic analysis suggested that Bupleurum yinchowense holds a distinct phylogenetic position and can be considered as an accepted species.
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Affiliation(s)
- Gaixia Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiuling Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fuhua Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Jin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiemei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Tian S, Lu P, Zhang Z, Wu JQ, Zhang H, Shen H. 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 DOI: 10.1186/s12864-021-07467-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
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Zhu B, Qian F, Hou Y, Yang W, Cai M, Wu X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS One 2021; 16:e0248556. [PMID: 33711072 PMCID: PMC7954331 DOI: 10.1371/journal.pone.0248556] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 12/05/2022] Open
Abstract
Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunfeng Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Weicheng Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xiaoming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Asaf S, Khan AL, Numan M, Al-Harrasi A. Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae. Sci Rep 2021; 11:3586. [PMID: 33574434 PMCID: PMC7878759 DOI: 10.1038/s41598-021-83060-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/14/2021] [Indexed: 01/30/2023] Open
Abstract
Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members' specifically A. marina and related species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Muhammad Numan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman
- Department of Biology, University of North Carolina at Greensboro, 363 Sullivan Science Building, NC, 27402-6170, USA
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
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Liu K, Wang R, Guo XX, Zhang XJ, Qu XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). Plants (Basel) 2021; 10:plants10010109. [PMID: 33419221 PMCID: PMC7825611 DOI: 10.3390/plants10010109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
Abstract
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.
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Affiliation(s)
| | | | | | | | - Xiao-Jian Qu
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
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Zhang Y, Li HL, Zhong JD, Wang Y, Yuan CC. Chloroplast Genome Sequences and Comparative Analyses of Combretaceae Mangroves with Related Species. Biomed Res Int 2020; 2020:5867673. [PMID: 33062686 DOI: 10.1155/2020/5867673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 11/17/2022]
Abstract
In the Combretaceae family, only two species of Lumnitzera and one species of Laguncularia belong to mangroves. Among them, Lumnitzera littorea (Jack) Voigt. is an endangered mangrove plant in China for the limited occurrence and seed abortion. In contrast, Lumnitzera racemosa Willd. is known as the most widespread mangrove plant in China. Laguncularia racemosa C. F. Gaertn., an exotic mangrove in China, has the fast growth and high adaptation ability. To better understand the phylogenetic positions of these mangroves in Combretaceae and in Myrtales and to provide information for studies on evolutionary adaptation for intertidal habitat, the complete chloroplast (cp) genomes of Lu. racemosa and La. racemosa were sequenced. Furthermore, we present here the results from the assembly and annotation of the two cp genomes, which were further subjected to the comparative analysis with Lu. littorea cp genomes we published before and other eleven closely related species within Myrtales. The chloroplast genomes of the three Combretaceae mangrove species: Lu. littorea, Lu. racemosa, and La. racemosa are 159,687 bp, 159,473 bp, and 158,311 bp in size. All three cp genomes host 130 genes including 85 protein-coding genes, 37 tRNAs, and 4 rRNAs. A comparative analysis of those three genomes revealed the high similarity of genes in coding-regions and conserved gene order in the IR and LSC/SSC regions. The differences between Lumnitzera and Laguncularia cp genomes are the locations of rps19 and rpl2 genes in the IR/SC boundary regions. Investigating the effects of selection events on shared protein-coding genes showed a relaxed selection had acted on the ycf2, ycf1, and matK genes of Combretaceae mangroves compared to the nonmangrove species Eucalyptus aromaphloia. The phylogenetic analysis based on the whole chloroplast genome sequence with one outgroup species strongly supported three Combretaceae mangroves together with other two Combretaceae species formed a cluster in Combretaceae. This study is the first report on the comparative analysis of three Combretaceae mangrove chloroplast genomes, which will provide the significant information for understanding photosynthesis and evolution in Combretaceae mangrove plants.
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Khayi S, Gaboun F, Pirro S, Tatusova T, El Mousadik A, Ghazal H, Mentag R. Complete Chloroplast Genome of Argania spinosa: Structural Organization and Phylogenetic Relationships in Sapotaceae. Plants (Basel) 2020; 9:E1354. [PMID: 33066261 PMCID: PMC7602116 DOI: 10.3390/plants9101354] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/02/2023]
Abstract
Argania spinosa (Sapotaceae), an important endemic Moroccan oil tree, is a primary source of argan oil, which has numerous dietary and medicinal proprieties. The plant species occupies the mid-western part of Morocco and provides great environmental and socioeconomic benefits. The complete chloroplast (cp) genome of A. spinosa was sequenced, assembled, and analyzed in comparison with those of two Sapotaceae members. The A. spinosa cp genome is 158,848 bp long, with an average GC content of 36.8%. The cp genome exhibits a typical quadripartite and circular structure consisting of a pair of inverted regions (IR) of 25,945 bp in length separating small single-copy (SSC) and large single-copy (LSC) regions of 18,591 and 88,367 bp, respectively. The annotation of A. spinosa cp genome predicted 130 genes, including 85 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. A total of 44 long repeats and 88 simple sequence repeats (SSR) divided into mononucleotides (76), dinucleotides (7), trinucleotides (3), tetranucleotides (1), and hexanucleotides (1) were identified in the A. spinosa cp genome. Phylogenetic analyses using the maximum likelihood (ML) method were performed based on 69 protein-coding genes from 11 species of Ericales. The results confirmed the close position of A. spinosa to the Sideroxylon genus, supporting the revisiting of its taxonomic status. The complete chloroplast genome sequence will be valuable for further studies on the conservation and breeding of this medicinally and culinary important species and also contribute to clarifying the phylogenetic position of the species within Sapotaceae.
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Affiliation(s)
- Slimane Khayi
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Fatima Gaboun
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD 20817, USA;
| | - Tatiana Tatusova
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20817, USA;
| | - Abdelhamid El Mousadik
- Laboratory of Biotechnology and Valorization of Natural Resources (LBVRN), Faculty of Sciences, University Ibn Zohr, Agadir 80000, Morocco;
| | - Hassan Ghazal
- National Center for Scientific and Technological Research (CNRST), Rabat 10102, Morocco;
| | - Rachid Mentag
- CRRA-Rabat, National Institute for Agricultural Research (INRA), Rabat 10101, Morocco;
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Liu L, Du Y, Shen C, Li R, Lee J, Li P. The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae. Genet Mol Biol 2020; 43:e20190272. [PMID: 32808964 PMCID: PMC7433754 DOI: 10.1590/1678-4685-gmb-2019-0272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 05/08/2020] [Indexed: 11/22/2022] Open
Abstract
Papaver setigerum is an annual herb that is closely related to the opium poppy, P. somniferum. Genetic resources for P. setigerum are scarce. In the present study, we assembled the complete chloroplast (cp) genome of P. setigerum based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of P. setigerum is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The rps15 gene has been lost from the genomes of Meconopsis racemosa, Coreanomecon hylomeconoides, P. orientale, P. somniferum, and P. setigerum, and the ycf15 gene is found only in C. hylomeconoides. Moreover, 13 cpDNA markers, including psbA-trnH, rps16-trnQ, trnS-trnG, trnC-petN, trnE-trnT, trnL-trnF, trnF-ndhJ, petA-psbJ, ndhF-rpl32, rpl32-trnL, ccsA-ndhD, ndhE-ndhG, and rps15-ycf1, were identified with relatively high levels of variation within Papaver, which will be useful for species identification in this genus. Among those markers, psbA-trnH is the best one to distinguish P. somniferum and P. setigerum.
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Affiliation(s)
- Luxian Liu
- Henan University, School of Life Sciences, Key Laboratory of
Plant Stress Biology, Kaifeng, China
| | - Yingxue Du
- Henan University, School of Life Sciences, Key Laboratory of
Plant Stress Biology, Kaifeng, China
| | - Cheng Shen
- Zhejiang University, College of Life Sciences, The Key
Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of
Education, Hangzhou, China
| | - Rui Li
- Food inspection and Testing Institute of Henan Province,
Physical and Chemical Laboratory, Zhengzhou, China
| | - Joongku Lee
- Chungnam National University, Department of Environment and
Forest Resources, Daejeon, South Korea
| | - Pan Li
- Zhejiang University, College of Life Sciences, The Key
Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of
Education, Hangzhou, China
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Liu J, Liu S, Wang R, Guan S, Qu J. Characterization of the complete chloroplast genome of Salix magnifica, a vulnerable species endemic to China. Mitochondrial DNA B Resour 2020; 5:2269-2270. [PMID: 33367003 PMCID: PMC7510628 DOI: 10.1080/23802359.2019.1710602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/23/2019] [Indexed: 11/23/2022] Open
Abstract
Salix magnifica is only sporadically distributed in the western part of Sichuan, the area of the willows is narrow. There are not many plants, and they easily fall into the endangered state. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of Salix magnifica by Illumina paired-end reads data. The whole genome was 154,977 bp, consisting of a pair of inverted repeats of 27,457 bp, large single-copy region, and a small single-copy region (71,119 and 16,205 bp in length, respectively). The cp genome contained 116 genes, including 80 protein-coding genes and 36 tRNA genes. The overall GC content of the whole genome was 36.7%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between Salix magnifica and Salix oreinoma.
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Affiliation(s)
- Jinfeng Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Siyan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Rui Wang
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- College of Life Sciences, Jilin Agricultural University, Changchun, China
| | - Jing Qu
- College of Life Sciences, Jilin Agricultural University, Changchun, China
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Ma Y, Jiao P, Qi Z, Jiang Z, Guan S. Characterization of the complete chloroplast genome of Alsophila spinulosa, an endangered species endemic to China. Mitochondrial DNA B Resour 2020; 5:2262-2263. [PMID: 33367000 PMCID: PMC7510675 DOI: 10.1080/23802359.2020.1772142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 11/08/2022] Open
Abstract
Tree fern Alsophila spinulosa is an endangered relic plant in the world. It is currently on the International Union for Conservation of Nature (IUCN) red list of threatened species. In this study, we first assembled the complete chloroplast (cp) genome of A. spinulosa by Illumina paired-end reads data. The whole genome was 156,661 bp, consisting of a pair of inverted repeats of 24,364 bp, large single copy region and a small single copy region (70,352 and 21,624 bp in length, respectively). The cp genome contained 133 genes, including 92 protein-coding genes, 33 trRNA genes, and eight rRNA genes. The overall GC content of the whole genome was 40.4%. A neighbour-joining phylogenetic analysis demonstrated a close relationship between A. spinulosa and Cystoathyrium chinense Ching.
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Affiliation(s)
- Yiyong Ma
- Jilin Agricultural University, Changchun, China
| | - Peng Jiao
- Jilin Agricultural University, Changchun, China
| | - Zhuo Qi
- Jilin Agricultural University, Changchun, China
| | | | - Shuyan Guan
- Jilin Agricultural University, Changchun, China
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Lim LWK, Chung HH, Hussain H. Complete chloroplast genome sequencing of sago palm (Metroxylon sagu Rottb.): Molecular structures, comparative analysis and evolutionary significance. Gene Reports 2020; 19:100662. [DOI: 10.1016/j.genrep.2020.100662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Feng S, Zheng K, Jiao K, Cai Y, Chen C, Mao Y, Wang L, Zhan X, Ying Q, Wang H. Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships. BMC Plant Biol 2020; 20:242. [PMID: 32466748 PMCID: PMC7254759 DOI: 10.1186/s12870-020-02429-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/03/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana. RESULTS The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value. CONCLUSION Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.
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Affiliation(s)
- Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Kaixin Zheng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
| | - Kaili Jiao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yuchen Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chuanlan Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yanyan Mao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Lingyan Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xiaori Zhan
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qicai Ying
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China
| | - Huizhong Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 311121, China.
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Li CJ, Wang RN, Li DZ. Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications. PLoS One 2020; 15:e0233167. [PMID: 32407424 PMCID: PMC7224561 DOI: 10.1371/journal.pone.0233167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
The conflicts exist between the phylogeny of Campanulaceae based on nuclear ITS sequence and plastid markers, particularly in the subdivision of Cyanantheae (Campanulaceae). Besides, various and complicated plastid genome structures can be found in species of the Campanulaceae. However, limited availability of genomic information largely hinders the studies of molecular evolution and phylogeny of Campanulaceae. We reported the complete plastid genomes of three Cyanantheae species, compared them to eight published Campanulaceae plastomes, and shed light on a deeper understanding of the applicability of plastomes. We found that there were obvious differences among gene order, GC content, gene compositions and IR junctions of LSC/IRa. Almost all protein-coding genes and amino acid sequences showed obvious codon preferences. We identified 14 genes with highly positively selected sites and branch-site model displayed 96 sites under potentially positive selection on the three lineages of phylogenetic tree. Phylogenetic analyses showed that Cyananthus was more closely related to Codonopsis compared with Cyclocodon and also clearly illustrated the relationship among the Cyanantheae species. We also found six coding regions having high nucleotide divergence value. Hotpot regions were considered to be useful molecular markers for resolving phylogenetic relationships and species authentication of Campanulaceae.
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Affiliation(s)
- Chun-Jiao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Nan Wang
- College of Life Sciences, Northwest University, Xi'an, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Asaf S, Khan AL, Khan A, Al-Harrasi A. Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. Int J Mol Sci 2020; 21:E3280. [PMID: 32384622 DOI: 10.3390/ijms21093280] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/14/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Genus Prosopis (family Fabaceae) are shrubby trees, native to arid and semi-arid regions of Asia, Africa, and America and known for nitrogen fixation. Here, we have sequenced the complete chloroplast (cp) genomes of two Prosopis species (P. juliflora and P. cineraria) and compared them with previously sequenced P. glandulosa, Adenanthera microsperma, and Parkia javanica belonging to the same family. The complete genome sequences of Prosopis species and related species ranged from 159,389 bp (A. microsperma) to 163,677 bp (P. cineraria). The overall GC contents of the genomes were almost the similar (35.9–36.6%). The P. juliflora and P. cineraria genomes encoded 132 and 131 genes, respectively, whereas both the species comprised of 85 protein-coding genes higher than other compared species. About 140, 134, and 129 repeats were identified in P. juliflora, P. cineraria and P. glandulosa cp genomes, respectively. Similarly, the maximum number of simple sequence repeats were determined in P. juliflora (88), P. cineraria (84), and P. glandulosa (78). Moreover, complete cp genome comparison determined a high degree of sequence similarity among P. juliflora, P. cineraria, and P. glandulosa, however some divergence in the intergenic spacers of A. microsperma and Parkia javanica were observed. The phylogenetic analysis showed that P. juliflora is closer to P. cineraria than P. glandulosa.
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Tyagi S, Jung JA, Kim JS, Won SY. Comparative Analysis of the Complete Chloroplast Genome of Mainland Aster spathulifolius and Other Aster Species. Plants (Basel) 2020; 9:E568. [PMID: 32365609 PMCID: PMC7285121 DOI: 10.3390/plants9050568] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
Aster spathulifolius, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland A. spathulifolius and compared it with those of the island type and other Aster species. The chloroplast genome of mainland A. spathulifolius is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two A. spathulifolius lines and the other Aster species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All Aster species clustered into a monophyletic group, but the chloroplast genome of mainland A. spathulifolius was more similar to the other Aster species than to that of the island A. spathulifolius. The accD and ndhF genes were detected to be under positive selection within the Aster lineage compared to other related taxa. The complete chloroplast genome of mainland A. spathulifolius presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the Aster genus and the Asteraceae.
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Affiliation(s)
- Swati Tyagi
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea;
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
| | - So Youn Won
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (S.T.); (J.S.K.)
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Li J, Xie DF, Guo XL, Zheng ZY, He XJ, Zhou SD. Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship. Plants (Basel) 2020; 9:E543. [PMID: 32331381 DOI: 10.3390/plants9040543] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/18/2020] [Accepted: 04/19/2020] [Indexed: 12/14/2022]
Abstract
Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.
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Xiong Y, Xiong Y, He J, Yu Q, Zhao J, Lei X, Dong Z, Yang J, Peng Y, Zhang X, Ma X. The Complete Chloroplast Genome of Two Important Annual Clover Species, Trifolium alexandrinum and T. resupinatum: Genome Structure, Comparative Analyses and Phylogenetic Relationships with Relatives in Leguminosae. Plants (Basel) 2020; 9:E478. [PMID: 32283660 PMCID: PMC7238141 DOI: 10.3390/plants9040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 01/31/2023]
Abstract
Trifolium L., which belongs to the IR lacking clade (IRLC), is one of the largest genera in the Leguminosae and contains several economically important fodder species. Here, we present whole chloroplast (cp) genome sequencing and annotation of two important annual grasses, Trifolium alexandrinum (Egyptian clover) and T. resupinatum (Persian clover). Abundant single nucleotide polymorphisms (SNPs) and insertions/deletions (In/Dels) were discovered between those two species. Global alignment of T. alexandrinum and T. resupinatum to a further thirteen Trifolium species revealed a large amount of rearrangement and repetitive events in these fifteen species. As hypothetical cp open reading frame (ORF) and RNA polymerase subunits, ycf1 and rpoC2 in the cp genomes both contain vast repetitive sequences and observed high Pi values (0.7008, 0.3982) between T. alexandrinum and T. resupinatum. Thus they could be considered as the candidate genes for phylogenetic analysis of Trifolium species. In addition, the divergence time of those IR lacking Trifolium species ranged from 84.8505 Mya to 4.7720 Mya. This study will provide insight into the evolution of Trifolium species.
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Affiliation(s)
- Yanli Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yi Xiong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jun He
- State Key Laboratory of Exploration and Utilization of Crop Gene Resources in 10 Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in 11 Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan 12 Agricultural University, Chengdu 600031, China;
| | - Qingqing Yu
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Junming Zhao
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiong Lei
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Zhixiao Dong
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Jian Yang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Yan Peng
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xinquan Zhang
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
| | - Xiao Ma
- College of Animal science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (Y.X.); (Q.Y.); (J.Z.); (X.L.); (Z.D.); (J.Y.); (Y.P.)
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Kamboj R, Singh B, Mondal TK, Bisht DS. Current status of genomic resources on wild relatives of rice. Breed Sci 2020; 70:135-144. [PMID: 32523396 PMCID: PMC7272243 DOI: 10.1270/jsbbs.19064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/26/2019] [Indexed: 06/02/2023]
Abstract
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
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Affiliation(s)
- Richa Kamboj
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Balwant Singh
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Tapan Kumar Mondal
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Deepak Singh Bisht
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
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Asaf S, Khan AL, Lubna, Khan A, Khan A, Khan G, Lee IJ, Al-Harrasi A. Expanded inverted repeat region with large scale inversion in the first complete plastid genome sequence of Plantago ovata. Sci Rep 2020; 10:3881. [PMID: 32127603 PMCID: PMC7054531 DOI: 10.1038/s41598-020-60803-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/17/2020] [Indexed: 11/09/2022] Open
Abstract
Plantago ovata (Plantaginaceae) is an economically and medicinally important species, however, least is known about its genomics and evolution. Here, we report the first complete plastome genome of P. ovata and comparison with previously published genomes of related species from Plantaginaceae. The results revealed that P. ovata plastome size was 162,116 bp and that it had typical quadripartite structure containing a large single copy region of 82,084 bp and small single copy region of 5,272 bp. The genome has a markedly higher inverted repeat (IR) size of 37.4 kb, suggesting large-scale inversion of 13.8 kb within the expanded IR regions. In addition, the P. ovata plastome contains 149 different genes, including 43 tRNA, 8 rRNA, and 98 protein-coding genes. The analysis revealed 139 microsatellites, of which 71 were in the non-coding regions. Approximately 32 forward, 34 tandem, and 17 palindromic repeats were detected. The complete genome sequences, 72 shared genes, matK gene, and rbcL gene from related species generated the same phylogenetic signals, and phylogenetic analysis revealed that P. ovata formed a single clade with P. maritima and P. media. The divergence time estimation as employed in BEAST revealed that P. ovata diverged from P. maritima and P. media about 11.0 million years ago (Mya; 95% highest posterior density, 10.06-12.25 Mya). In conclusion, P. ovata had significant variation in the IR region, suggesting a more stable P. ovata plastome genome than that of other Plantaginaceae species.
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Affiliation(s)
- Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
| | - Lubna
- Department of Botany, Garden Campus, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Arif Khan
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, 8049, Norway
| | - Gulzar Khan
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University, Oldenburg, Oldenburg, Germany
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman.
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Li C, Zhao Y, Xu Z, Yang G, Peng J, Peng X. Initial Characterization of the Chloroplast Genome of Vicia sepium, an Important Wild Resource Plant, and Related Inferences About Its Evolution. Front Genet 2020; 11:73. [PMID: 32153639 PMCID: PMC7044246 DOI: 10.3389/fgene.2020.00073] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/22/2020] [Indexed: 01/29/2023] Open
Abstract
Lack of complete genomic information concerning Vicia sepium (Fabaceae: Fabeae) precludes investigations of evolution and populational diversity of this perennial high-protein forage plant suitable for cultivation in extreme conditions. Here, we present the complete and annotated chloroplast genome of this important wild resource plant. V. sepium chloroplast genome includes 76 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 1 pseudogene. Its 124,095 bp sequence has a loss of one inverted repeat (IR). The GC content of the whole genome, the protein-coding, intron, tRNA, rRNA, and intergenic spacer regions was 35.0%, 36.7%, 34.6%, 52.3%, 54.2%, and 29.2%, respectively. Comparative analyses with plastids from related genera belonging to Fabeae demonstrated that the greatest variation in the V. sepium genome length occurred in protein-coding regions. In these regions, some genes and introns were lost or gained; for example, ycf4, clpP intron, and rpl16 intron deletions and rpl20 and ORF292 insertions were observed. Twelve highly divergent regions, 66 simple sequence repeats (SSRs) and 27 repeat sequences were also found in these regions. Detailed evolutionary rate analysis of protein-coding genes showed that Vicia species exhibit additional interesting characteristics including positive selection of ccsA, clpP, rpl32, rpl33, rpoC1, rps15, rps2, rps4, and rps7, and the evolutionary rates of atpA, accD, and rps2 in Vicia are significantly accelerated. These genes are important candidate genes for understanding the evolutionary strategies of Vicia and other genera in Fabeae. The phylogenetic analysis showed that Vicia and Lens are included in the same clade and that Vicia is paraphyletic. These results provide evidence regarding the evolutionary history of the chloroplast genome.
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Affiliation(s)
- Chaoyang Li
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
- Hunan Urban and Rural Ecological Planning and Restoration Engineering Research Center, Hunan City University, Yiyang, China
| | - Guiyan Yang
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, China
| | - Xiaoyun Peng
- Hunan Urban and Rural Ecological Planning and Restoration Engineering Research Center, Hunan City University, Yiyang, China
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Khan A, Asaf S, Khan AL, Shehzad T, Al-Rawahi A, Al-Harrasi A. Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny. Plants (Basel) 2020; 9:plants9020199. [PMID: 32033491 PMCID: PMC7076480 DOI: 10.3390/plants9020199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 11/30/2022]
Abstract
Euphorbia is one of the largest genera in the Euphorbiaceae family, comprising 2000 species possessing commercial, medicinal, and ornamental importance. However, there are very little data available on their molecular phylogeny and genomics, and uncertainties still exist at a taxonomic level. Herein, we sequence the complete chloroplast (cp) genomes of two species, E. larica and E. smithii, of the genus Euphorbia through next-generation sequencing and perform a comparative analysis with nine related genomes in the family. The results revealed that the cp genomes had similar quadripartite structure, gene content, and genome organization with previously reported genomes from the same family. The size of cp genomes ranged from 162,172 to 162,358 bp with 132 and 133 genes, 8 rRNAs, 39 tRNA in E. smithii and E. larica, respectively. The numbers of protein-coding genes were 85 and 86, with each containing 19 introns. The four-junction regions were studied and results reveal that rps19 was present at JLB (large single copy region and inverted repeat b junction) in E. larica where its complete presence was located in the IRb (inverted repeat b) region in E. smithii. The sequence comparison revealed that highly divergent regions in rpoC1, rpocB, ycf3, clpP, petD, ycf1, and ndhF of the cp genomes might provide better understanding of phylogenetic inferences in the Euphorbiaceae and order Malpighiales. Phylogenetic analyses of this study illustrate sister clades of E. smithii with E. tricullii and these species form a monophyletic clade with E. larica. The current study might help us to understand the genome architecture, genetic diversity among populations, and evolutionary depiction in the genera.
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Affiliation(s)
- Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.K.); (S.A.); (A.A.-R.)
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.K.); (S.A.); (A.A.-R.)
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.K.); (S.A.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
| | - Tariq Shehzad
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, 2713 Doha, Qatar;
| | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.K.); (S.A.); (A.A.-R.)
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Oman; (A.K.); (S.A.); (A.A.-R.)
- Correspondence: (A.L.K.); (A.A.-H.)
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50
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Ni Z, Ye Y, Xu M, Xu LA. Comparison among three methods for obtaining chloroplast genome sequences from the conifer Pinus massoniana. Genomics 2020; 112:2459-2466. [PMID: 32014522 DOI: 10.1016/j.ygeno.2020.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/03/2020] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The chloroplast genome (CPG) is a powerful tool for phylogenetic studies. Many CPGs have been determined using NGS. However, the large nuclear-genome and difficult CPG-DNA separation in conifers limit their application in related research. In this study, three methods (PCR + Sanger, PCR + HiSeq, cpDNA+HiSeq) for obtaining the CPGs of Pinus massoniana were compared for sequence accuracy, time and cost. PCR + Sanger obtained the most accurate CPGs with advantages in cost (3.08$/kb) and time (2-3 days); PCR + HiSeq generated some DNA fragments with low depth, and the SNPs false-positive-rate (0.44) and sequencing error-rate (0.0265) of this method were higher than those of the cpDNA+HiSeq. Moreover, the cost (~6.17$/kb) and time (4-5 weeks) would significantly increase when HiSeq sequencing were outsourced to sequencing service company. Thus, for the study of intraspecific and interspecies variation in CPGs, CPG sequences can be obtained by comprehensive methods to bridge the method shortcomings. Scuh as sequence accuracy, cost and time.
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Affiliation(s)
- ZhouXian Ni
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - YouJu Ye
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Li-An Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China..
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