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González-Trillo AC, Reyes López MÁ, Almaraz-Abarca N, Herrera-Arrieta Y, Gutiérrez-Velázquez MV, Barraza Salas M, Monreal-García HM, Torres-Ricario R. Characterization of the complete chloroplast genome sequence of Agave durangensis (Asparagales: Asparagaceae: Agavoideae). Mitochondrial DNA B Resour 2024; 9:536-540. [PMID: 38655148 PMCID: PMC11036899 DOI: 10.1080/23802359.2024.2338546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 03/31/2024] [Indexed: 04/26/2024] Open
Abstract
Agave durangensis commonly known as agave cenizo, is an endemic Agave species in Mexico used for mescal production, yet its taxonomic delimitation is still controversial. This study aimed to enhance taxonomic clarity by characterizing its chloroplast genome. Chloroplast DNA was isolated from 2-year-old A. durangensis leaves. The complete chloroplast genome size was 156,441 bp, comprising a large single-copy region (LSC), a pair of inverted repeat regions (IR), and a small single-copy region (SSC). Annotation revealed 87 protein-coding genes, 38 tRNAs, and 8 rRNAs, with notable gene inversions. Phylogenetic analysis suggests, A. durangensis forms a separate lineage within the Agave genus.
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Affiliation(s)
| | | | | | | | | | - Marcelo Barraza Salas
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Durango, Mexico
| | - Hugo Manuel Monreal-García
- Instituto Politécnico Nacional CIIDIR Unidad Durango, Durango, Durango, Mexico
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Durango, Mexico
| | - Rene Torres-Ricario
- Instituto Politécnico Nacional CIIDIR Unidad Durango, Durango, Durango, Mexico
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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Tian Y, Liu X, Xu Y, Yu B, Wang L, Qu X. Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots. Sci Rep 2023; 13:15622. [PMID: 37730791 PMCID: PMC10511529 DOI: 10.1038/s41598-023-42945-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/16/2023] [Indexed: 09/22/2023] Open
Abstract
Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.
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Affiliation(s)
- Yulu Tian
- School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, No. 1166 Liutai Avenue, Wenjiang District, Chengdu, 611137, China
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Xue Liu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
| | - Yuanjiang Xu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Benxia Yu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China
| | - Le Wang
- College of Life Science and Food Engineering, Chongqing Three Gorges University, 666 Tianxing Road, Wanzhou District, Chongqing, 404100, China
| | - Xianyou Qu
- Chongqing Academy of Chinese Materia Medica, 34 Nanshan Road, Huangjueya, Nanan District, Chongqing, 400065, China.
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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. [PMID: 36474705 PMCID: PMC9684740 DOI: 10.1515/biol-2022-0497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 09/08/2024] Open
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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Sheng W. The entire chloroplast genome sequence of Asparagus cochinchinensis and genetic comparison to Asparagus species. Open Life Sci 2022; 17:893-906. [PMID: 36045717 PMCID: PMC9372710 DOI: 10.1515/biol-2022-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/01/2022] [Accepted: 05/18/2022] [Indexed: 11/15/2022] Open
Abstract
Asparagus cochinchinensis is a traditional Chinese medicinal plant. The chloroplast (cp) genome study on A. cochinchinensis is poorly understood. In this research, we collected the data from the cp genome assembly and gene annotation of A. cochinchinensis, followed by further comparative analysis with six species in the genus Asparagus. The cp genome of A. cochinchinensis showed a circular quadripartite structure in the size of 157,095 bp, comprising a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions. A total of 137 genes were annotated, consisting of 86 protein-coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 5 pseudo-genes. Forty scattered repetitive sequences and 247 simple sequence repeats loci were marked out. In addition, A/T-ending codons were shown to have a basis in the codon analysis. A cp genome comparative analysis revealed that a similar gene composition was detected in the IR and LSC/SSC regions with Asparagus species. Based on the complete cp genome sequence in Asparagaceae, the result showed that A. cochinchinensis was closely related to A. racemosus by phylogenetic analysis. Therefore, our study providing A. cochinchinensis genomic resources could effectively contribute to the phylogenetic analysis and molecular identification of the genus Asparagus.
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Affiliation(s)
- Wentao Sheng
- Department of Biological Technology, Nanchang Normal University, Nanchang 330032, Jiangxi, China
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Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.). FORESTS 2022. [DOI: 10.3390/f13060932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Socotra dragon`s blood tree (Dracaena cinnabari Balf.) is endemic to the island of Socotra in Yemen. This iconic species plays an essential role in the survival of associated organisms, acting as an umbrella tree. Overexploitation, overgrazing by livestock, global climate change, and insufficient regeneration mean that the populations of this valuable species are declining in the wild. Although there are many studies on the morphology, anatomy, and physiology of D. cinnabari, no genomic analysis of this endangered species has been performed so far. Therefore, the main aim of this study was to characterize the complete chloroplast sequence genome of D. cinnabari for conservation purposes. The D. cinnabari chloroplast genome is 155,371 bp with a total GC content of 37.5%. It has a quadripartite plastid genome structure composed of one large single-copy region of 83,870 bp, one small single-copy region of 18,471 bp, and two inverted repeat regions of 26,515 bp each. One hundred and thirty-two genes were annotated, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Forty simple sequence repeats have also been identified in this chloroplast genome. Comparative analysis of complete sequences of D. cinnabari chloroplast genomes with other species of the genus Dracaena showed a very high conservativeness of their structure and organization. Phylogenetic inference showed that D. cinnabari is much closer to D. draco, D. cochinchinensis, and D. cambodiana than to D. terniflora, D. angustifolia, D. hokouensis, and D. elliptica. The results obtained in this study provide new and valuable omics data for further phylogenetic studies of the genus Dracaena as well as enable the protection of genetic resources of highly endangered D. cinnabari.
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Wong KH, Kong BLH, Siu TY, Wu HY, But GWC, Shaw P, Lau DTW. Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics. PLoS One 2022; 17:e0266376. [PMID: 35468142 PMCID: PMC9037925 DOI: 10.1371/journal.pone.0266376] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/19/2022] [Indexed: 11/21/2022] Open
Abstract
Asparagus species are widely used for medicinal, horticultural, and culinary purposes. Complete chloroplast DNA (cpDNA) genomes of three Asparagus specimens collected in Hong Kong-A. aethiopicus, A. densiflorus 'Myers', and A. cochinchinensis-were de novo assembled using Illumina sequencing. Their sizes ranged from 157,069 to 157,319 bp, with a total guanine-cytosine content of 37.5%. Structurally, a large single copy (84,598-85,350 bp) and a small single copy (18,677-18,685 bp) were separated by a pair of inverted repeats (26,518-26,573 bp). In total, 136 genes were annotated for A. aethiopicus and A. densiflorus 'Myers'; these included 90 mRNA, 38 tRNA, and 8 rRNA genes. Further, 132 genes, including 87 mRNA, 37 tRNA, and 8 rRNA genes, were annotated for A. cochinchinensis. For comparative and phylogenetic analysis, we included NCBI data for four congenerics, A. setaceus, A. racemosus, A. schoberioides, and A. officinalis. The gene content, order, and genome structure were relatively conserved among the genomes studied. There were similarities in simple sequence repeats in terms of repeat type, sequence complementarity, and cpDNA partition distribution. A. densiflorus 'Myers' had distinctive long sequence repeats in terms of their quantity, type, and length-interval frequency. Divergence hotspots, with nucleotide diversity (Pi) ≥ 0.015, were identified in five genomic regions: accD-psaI, ccsA, trnS-trnG, ycf1, and ndhC-trnV. Here, we summarise the historical changes in the generic subdivision of Asparagus. Our phylogenetic analysis, which also elucidates the nomenclatural complexity of A. aethiopicus and A. densiflorus 'Myers', further supports their close phylogenetic relationship. The findings are consistent with prior generic subdivisions, except for the placement of A. racemosus, which requires further study. These de novo assembled cpDNA genomes contribute valuable genomic resources and help to elucidate Asparagus taxonomy.
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Affiliation(s)
- Kwan-Ho Wong
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Bobby Lim-Ho Kong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Tin-Yan Siu
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - Pang‑Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
| | - David Tai-Wai Lau
- Shiu-Ying Hu Herbarium, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, the People’s Republic of China
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Li SF, Wang J, Dong R, Zhu HW, Lan LN, Zhang YL, Li N, Deng CL, Gao WJ. Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus. HORTICULTURE RESEARCH 2020; 7:48. [PMID: 32257234 PMCID: PMC7109074 DOI: 10.1038/s41438-020-0271-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 05/04/2023]
Abstract
Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of A. setaceus to facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly of A. setaceus covering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome of A. setaceus was predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time of A. setaceus from its close relative A. officinalis of ~9.66 million years ago, and A. setaceus underwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted in A. setaceus. These findings provide new knowledge about the characteristics and evolution of the A. setaceus genome, and will facilitate comparative genetic and genomic research on the genus Asparagus.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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