1
|
Liu H, Xie K, Hua D. The complete chloroplast genome of Pyankovia brachiata (amaranthaceae), an annual desert plant in China. Mitochondrial DNA B Resour 2024; 9:1112-1116. [PMID: 39165386 PMCID: PMC11334741 DOI: 10.1080/23802359.2024.2393469] [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: 06/21/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
Pyankovia brachiata (Pall.) Akhani & Roalson 2007, is an annual plant belonging to the genus Pyankovia, family Amaranthaceae, which is widely distributed in the inland deserts of Northwest China. P. brachiata was previously categorized under the genus Salsola in Salsoleae and has been a long-standing topic of debate. Therefore, the complete chloroplast genome of P. brachiata must be studied to provide a theoretical reference for species classification. In this study, we sequenced P. brachiata samples and determined the species' complete chloroplast genome. The complete chloroplast genome was 149,922 bp in length, with one large single copy (LSC: 83,565 bp), one small single copy (SSC: 18,535 bp), and two inverted repeat regions (IRa and IRb, 23,911 bp each). It contains 132 genes, including 87 protein-coding, eight rRNA, and 37 tRNA genes. The phylogenetic position showed that P. brachiata has the closest relationship with Caroxylon passerinum (accession number: NC057191.1). This study will provide genetic information and be beneficial to understanding the systematic position of P. brachiata within the Amaranthaceae.
Collapse
Affiliation(s)
- Huafeng Liu
- College of Life Sciences, China West Normal University, Nanchong, China
| | - Kaiqing Xie
- College of Grassland Science, Xinjiang Agricultural University, Urumqi, China
| | - Donglai Hua
- College of Life Science and Biotechnology, Mianyang Normal University, Mianyang, China
| |
Collapse
|
2
|
Wan H, Fu W, Zhu Z, Zhang Q, Li Y, Long L, Li L. Characterization of the complete chloroplast genome sequence of Bassia scoparia (L.) A. J. Scott 1978 (Amaranthaceae) and its phylogenetic analysis. Mitochondrial DNA B Resour 2024; 9:787-792. [PMID: 38903543 PMCID: PMC11188946 DOI: 10.1080/23802359.2024.2364959] [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: 02/05/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.
Collapse
Affiliation(s)
- Haiying Wan
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Wei Fu
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Zhenxing Zhu
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Qiaohui Zhang
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Yajie Li
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Lan Long
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| | - Lin Li
- Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, China
| |
Collapse
|
3
|
Alshegaihi RM. The complete chloroplast genome of the halophyte flowering plant Suaeda monoica from Jeddah, Saudi Arabia. Mol Biol Rep 2024; 51:60. [PMID: 38165474 DOI: 10.1007/s11033-023-09069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/11/2023] [Indexed: 01/03/2024]
Abstract
The complete chloroplast genome (plastome) of the annual flowering halophyte herb Suaeda monoica Forssk. ex J. F. Gmel. family (Amaranthaceae) that grows in Jeddah, Saudi Arabia, was identified for the first time in this study. Suaeda monoica is a medicinal plant species whose taxonomic classification remains controversial. Further, studying the species is useful for current conservation and management efforts. In the current study, the full chloroplast genome S. monoica was reassembled using whole-genome next-generation sequencing and compared with the previously published chloroplast genomes of Suaeda species. The chloroplast genome size of Suaeda monoica was 151,789 bp, with a single large copy of 83,404 bp, a small single copy of 18,007 bp and two inverted repeats regions of 25,189 bp. GC content in the whole genome was 36.4%. The cp genome included 87 genes that coded for proteins, 37 genes coding for tRNA, 8 genes coding for rRNA and one non-coding pseudogene. Five chloroplast genome features were compared between S. monoica and S. japonica, S. glauca, S. salsa, S. malacosperma and S. physophora. Among Suaeda genus and equal to most angiosperms chloroplast genomes, the RSCU values were conservative. Two pseudogenes (accD and ycf1), rpl16 intron and ndhF-rpl32 intergenic spacer, were highlighted as suitable DNA barcodes for different Suaeda species. Phylogenetic analyses show Suaeda cluster into three main groups; one in which S. monoica was closer to S. salsa. The obtained result provided valuable information on the characteristics of the S. monoica chloroplast genome and the phylogenetic relationships.
Collapse
Affiliation(s)
- Rana M Alshegaihi
- Department of Biological Sciences, College of Science, University of Jeddah, 21493, Jeddah, Saudi Arabia.
| |
Collapse
|
4
|
The Comparative Analyses of Six Complete Chloroplast Genomes of Morphologically Diverse Chenopodium album L. (Amaranthaceae) Collected in Korea. Int J Genomics 2021; 2021:6643444. [PMID: 33996994 PMCID: PMC8096589 DOI: 10.1155/2021/6643444] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/09/2021] [Indexed: 01/16/2023] Open
Abstract
Chenopodium album sensu stricto belonging to C. album aggregate is an annual cosmopolitan weed displaying the diversity of morphologies. We completed the six chloroplast genomes of C. album s. str. collected in Korea to understand the relationship between the diversity of chloroplast genomes and their morphological variations. All six C. album chloroplast genomes have a typical quadripartite structure with length ranging from 151,906 bp to 152,199 bp, similar to the previously sequenced C. album chloroplast genome (NC_034950). In total, 56 single nucleotide polymorphisms (SNPs) and 26 insertion and deletion (INDEL) regions (308 bp in total) were identified from the six chloroplast genomes, presenting a low level of intraspecific variations in comparison to the other angiosperm species. 376 normal simple sequence repeats were identified in all seven C. album chloroplast genomes. The phylogenetic analysis based on all available complete Amaranthaceae chloroplast genomes presents phylogenetic positions of six C. album samples as well as correlation with one of C. album morphological features. Our results provide the way to investigate intraspecific features of C. album chloroplast genomes and also the insights of understanding various intraspecific characteristics including morphological features.
Collapse
|
5
|
Park JS, Jin DP, Choi BH. Insights into genomic structure and evolutionary processes of coastal Suaeda species in East Asia using cpDNA, nDNA, and genome-wide SNPs. Sci Rep 2020; 10:20950. [PMID: 33262390 PMCID: PMC7708624 DOI: 10.1038/s41598-020-78041-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/27/2020] [Indexed: 11/30/2022] Open
Abstract
Species in the genus Suaeda have few diagnostic characters and substantial morphological plasticity. Hence, regional floras do not provide clear taxonomic information for Suaeda spp. in East Asia. In order to assess the taxonomy of four species in the genus Suaeda (S. australis, S. maritima, S. japonica, and S. heteroptera), cpDNA (rpl32-trnL and trnH-psbA), nDNA (ITS), and MIG-seq analyses were carried out. Genome-wide SNP results indicated three lineages: (1) S. australis in Korea and S. maritima in Japan, (2) S. maritima in Korea and S. heteroptera in China, and (3) S. japionica. In phylogenetic trees and genotype analyses, cpDNA and nDNA results showed discrepancies, while S. japonica and S. maritima in Korea, and S. heteroptera in China shared the same haplotype and ribotype. We suggest that the shared haplotype may be due to chloroplast capture. Based on our results, we assume that S. japonica was formed by homoploid hybrid speciation between the two lineages.
Collapse
Affiliation(s)
- Jong-Soo Park
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea
| | - Byoung-Hee Choi
- Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea.
| |
Collapse
|
6
|
Sharpe RM, Williamson-Benavides B, Edwards GE, Dhingra A. Methods of analysis of chloroplast genomes of C 3, Kranz type C 4 and Single Cell C 4 photosynthetic members of Chenopodiaceae. PLANT METHODS 2020; 16:119. [PMID: 32874195 PMCID: PMC7457496 DOI: 10.1186/s13007-020-00662-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C3 photosynthesis, and variations of C4 photosynthesis in which photorespiration is reduced by concentrating CO2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C4 species, and greatest structural and biochemical diversity in forms of C4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. RESULTS Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C3, Kranz type C4 and single cell C4 (SSC4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. CONCLUSIONS This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region sequences. Therefore, the use of high throughput and Sanger sequencing, in a hybrid method, reaffirms to be rapid, efficient, and reliable for chloroplast genome sequencing.
Collapse
Affiliation(s)
- Richard M. Sharpe
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Bruce Williamson-Benavides
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
| | - Gerald E. Edwards
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164 USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
- Molecular Plants Sciences, Washington State University, Pullman, WA 99164 USA
| |
Collapse
|
7
|
Kim Y, Park J, Chung Y. The comparison of the complete chloroplast genome of Suaeda japonica Makino presenting different external morphology (Amaranthaceae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1715867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Yongsung Kim
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd, Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Youngjae Chung
- Department of Biology, Shingyeong University, Gyeonggi-do, Republic of Korea
| |
Collapse
|
8
|
Mangelson H, Jarvis DE, Mollinedo P, Rollano‐Penaloza OM, Palma‐Encinas VD, Gomez‐Pando LR, Jellen EN, Maughan PJ. The genome of Chenopodium pallidicaule: An emerging Andean super grain. APPLICATIONS IN PLANT SCIENCES 2019; 7:e11300. [PMID: 31832282 PMCID: PMC6858295 DOI: 10.1002/aps3.11300] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/24/2019] [Indexed: 05/28/2023]
Abstract
PREMISE Cañahua is a semi-domesticated crop grown in high-altitude regions of the Andes. It is an A-genome diploid (2n = 2x = 18) relative of the allotetraploid (AABB) Chenopodium quinoa and shares many of its nutritional benefits. Cañahua seed contains a complete protein, a low glycemic index, and offers a wide variety of nutritionally important vitamins and minerals. METHODS The reference assembly was developed using a combination of short- and long-read sequencing techniques, including multiple rounds of Hi-C-based proximity-guided assembly. RESULTS The final assembly of the ~363-Mbp genome consists of 4633 scaffolds, with 96.6% of the assembly contained in nine scaffolds representing the nine haploid chromosomes of the species. Repetitive element analysis classified 52.3% of the assembly as repetitive, with the most common repeat identified as long terminal repeat retrotransposons. MAKER annotation of the final assembly yielded 22,832 putative gene models. DISCUSSION When compared with quinoa, strong patterns of synteny support the hypothesis that cañahua is a close A-genome diploid relative, and thus potentially a simplified model diploid species for genetic analysis and improvement of quinoa. Resequencing and phylogenetic analysis of a diversity panel of cañahua accessions suggests that coordinated efforts are needed to enhance genetic diversity conservation within ex situ germplasm collections.
Collapse
Affiliation(s)
- Hayley Mangelson
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - David E. Jarvis
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - Patricia Mollinedo
- Institute of Natural Product ResearchUniversidad Mayor de San AndrésLa PazBolivia
| | | | | | - Luz Rayda Gomez‐Pando
- Departamento de FitotecniaFacultad de AgronomíaUniversidad Nacional Agraria de La MolinaLa MolinaPeru
| | - Eric N. Jellen
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| | - Peter J. Maughan
- Department of Plant and Wildlife SciencesBrigham Young University5144 LSBProvoUtah84602USA
| |
Collapse
|
9
|
Maughan PJ, Chaney L, Lightfoot DJ, Cox BJ, Tester M, Jellen EN, Jarvis DE. Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.). Sci Rep 2019; 9:185. [PMID: 30655548 PMCID: PMC6336861 DOI: 10.1038/s41598-018-36693-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/23/2018] [Indexed: 11/18/2022] Open
Abstract
Quinoa has recently gained international attention because of its nutritious seeds, prompting the expansion of its cultivation into new areas in which it was not originally selected as a crop. Improving quinoa production in these areas will benefit from the introduction of advantageous traits from free-living relatives that are native to these, or similar, environments. As part of an ongoing effort to characterize the primary and secondary germplasm pools for quinoa, we report the complete mitochondrial and chloroplast genome sequences of quinoa accession PI 614886 and the identification of sequence variants in additional accessions from quinoa and related species. This is the first reported mitochondrial genome assembly in the genus Chenopodium. Inference of phylogenetic relationships among Chenopodium species based on mitochondrial and chloroplast variants supports the hypotheses that 1) the A-genome ancestor was the cytoplasmic donor in the original tetraploidization event, and 2) highland and coastal quinoas were independently domesticated.
Collapse
Affiliation(s)
- Peter J Maughan
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Lindsay Chaney
- Snow College, Department of Biological Sciences, Division of Natural Science and Mathematics, Ephraim, Utah, 84627, USA
| | - Damien J Lightfoot
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Brian J Cox
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - Mark Tester
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - Eric N Jellen
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA
| | - David E Jarvis
- Brigham Young University, Department of Plant and Wildlife Sciences, College of Life Sciences, Provo, Utah 84602, USA.
| |
Collapse
|
10
|
Kim Y, Park J, Chung Y. The complete chloroplast genome of Suaeda japonica Makino (Amaranthaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1601039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yongsung Kim
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Gangnam-gu, Republic of Korea
- InfoBoss Research Center, Seoul, Gangnam-gu, Republic of Korea
| | - Youngjae Chung
- Department of Biology, Shingyeong University, Gyeonggi-do, Hwaseong-si, Republic of Korea
| |
Collapse
|