1
|
Cao Z, Qu Y, Song Y, Xin P. Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae). Gene 2024; 907:148259. [PMID: 38346458 DOI: 10.1016/j.gene.2024.148259] [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: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/20/2024]
Abstract
The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.
Collapse
Affiliation(s)
- Zhengying Cao
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yaya Qu
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China
| | - Yu Song
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education), Guangxi Normal University, Guilin, Guangxi, China; Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China.
| | - Peiyao Xin
- Southwest Research Center for Landscape Architecture Engineering, National Forestry and Grassland Administration, Southwest Forestry University, Kunming, China; Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Southwest Forestry University, Kunming, China.
| |
Collapse
|
2
|
Yang S, Chen J, Li Z, Huang X, Zhang X, Liu Q, Tojibaev K, Sun H, Deng T. Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships. BMC Plant Biol 2024; 24:350. [PMID: 38684982 PMCID: PMC11059739 DOI: 10.1186/s12870-024-04989-7] [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] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/04/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time. RESULTS The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections. CONCLUSIONS This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.
Collapse
Affiliation(s)
- Shunquan Yang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Juntong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhimin Li
- School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Xianhan Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qun Liu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Komiljon Tojibaev
- Institute of Botany, Academy Sciences of Uzbekistan, Tashkent, 100125, Uzbekistan
| | - Hang Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Tao Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
3
|
Kan J, Zhang S, Wu Z, Bi D. Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics. Genes (Basel) 2024; 15:441. [PMID: 38674377 PMCID: PMC11049882 DOI: 10.3390/genes15040441] [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: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.
Collapse
Affiliation(s)
- Junhu Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| |
Collapse
|
4
|
Gao Y, Chen T, Long J, Shen G, Tian Z. Complete chloroplast genome and comparison of herbicides toxicity on Aeschynomene indica (Leguminosae) in upland direct-seeding paddy field. BMC Genomics 2024; 25:277. [PMID: 38486176 PMCID: PMC10938726 DOI: 10.1186/s12864-024-10102-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Indian jointvetch (Aeschynomene indica) is a common and pernicious weed found in the upland direct-seeding rice fields in the lower reaches of the Yangtze River in China. However, there are few reports on the degree of harm, genetic characteristics, and management methods of this weed. The purpose of this study is to clarify the harm of Indian jointvetch to upland direct-seeding rice, analyze the genetic characteristics of this weed based on chloroplast genomics and identify its related species, and screen herbicides that are effective in managing this weed in upland direct-seeding rice fields. RESULTS In a field investigation in upland direct-seeding rice paddies in Shanghai and Jiangsu, we determined that the plant height and maximum lateral distance of Indian jointvetch reached approximately 134.2 cm and 57.9 cm, respectively. With Indian jointvetch present at a density of 4/m2 and 8/m2, the yield of rice decreased by approximately 50% and 70%, respectively. We further obtained the first assembly of the complete chloroplast (cp.) genome sequence of Indian jointvetch (163,613 bp). There were 161 simple sequence repeats, 166 long repeats, and 83 protein-encoding genes. The phylogenetic tree and inverted repeat region expansion and contraction analysis based on cp. genomes demonstrated that species with closer affinity to A. indica included Glycine soja, Glycine max, and Sesbania cannabina. Moreover, a total of 3281, 3840, and 3838 single nucleotide polymorphisms were detected in the coding sequence regions of the cp. genomes of S. cannabina voucher IBSC, G. soja, and G. max compared with the A. indica sequence, respectively. A greenhouse pot experiment indicated that two pre-emergence herbicides, saflufenacil and oxyfluorfen, and two post-emergence herbicides, florpyrauxifen-benzyl and penoxsulam, can more effectively manage Indian jointvetch than other common herbicides in paddy fields. The combination of these two types of herbicides is recommended for managing Indian jointvetch throughout the entire growth period of upland direct-seeding rice. CONCLUSIONS This study provides molecular resources for future research focusing on the identification of the infrageneric taxa, phylogenetic resolution, and biodiversity of Leguminosae plants, along with recommendations for reliable management methods to control Indian jointvetch.
Collapse
Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China
| | - TianYu Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418, Shanghai, China
| | - Jiaqi Long
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418, Shanghai, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China.
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, 201403, Shanghai, China.
| |
Collapse
|
5
|
Ran Z, Li Z, Xiao X, An M, Yan C. Complete chloroplast genomes of 13 species of sect. Tuberculata Chang (Camellia L.): genomic features, comparative analysis, and phylogenetic relationships. BMC Genomics 2024; 25:108. [PMID: 38267876 PMCID: PMC10809650 DOI: 10.1186/s12864-024-09982-w] [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: 06/16/2023] [Accepted: 01/06/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Sect. Tuberculata belongs to Camellia, and its members are characterized by a wrinkled pericarp and united filaments. All the plants in this group, which are endemic to China, are highly valuable for exploring the evolution of Camellia and have great potential for use as an oil source. However, due to the complex and diverse phenotypes of these species and the difficulty of investigating them in the field, their complex evolutionary history and interspecific definitions have remained largely unelucidated. RESULTS Therefore, we newly sequenced and annotated 12 chloroplast (cp) genomes and retrieved the published cp genome of Camellia anlungensis Chang in sect. Tuberculata. In this study, comparative analysis of the cp genomes of the thirteen sect. Tuberculata species revealed a typical quadripartite structure characterized by a total sequence length ranging from 156,587 bp to 157,068 bp. The cp.genome arrangement is highly conserved and moderately differentiated. A total of 130 to 136 genes specific to the three types were identified by annotation, including protein-coding genes (coding sequences (CDSs)) (87-91), tRNA genes (35-37), and rRNA genes (8). The total observed frequency ranged from 23,045 (C. lipingensis) to 26,557 (C. anlungensis). IR region boundaries were analyzed to show that the ycf1 gene of C. anlungensis is located in the IRb region, while the remaining species are present only in the IRa region. Sequence variation in the SSC region is greater than that in the IR region, and most protein-coding genes have high codon preferences. Comparative analyses revealed six hotspot regions (tRNA-Thr(GGT)-psbD, psbE-petL, ycf15-tRNA-Leu(CAA), ndhF-rpl32, ndhD, and trnL(CAA)-ycf15) in the cp genomes that could serve as potential molecular markers. In addition, the results of phylogenetic tree construction based on the cp genomes showed that the thirteen sect. Tuberculata species formed a monophyletic group and were divided into two evolutionarily independent clades, confirming the independence of the section. CONCLUSIONS In summary, we obtained the cp genomes of thirteen sect. Tuberculata plants and performed the first comparative analysis of this group. These results will help us better characterize the plants in this section, deepen our understanding of their genetic characteristics and phylogenetic relationships, and lay the theoretical foundation for their accurate classification, elucidation of their evolutionary changes, and rational development and utilization of this section in the future.
Collapse
Affiliation(s)
- Zhaohui Ran
- College of Forestry, Guizhou University, Guiyang, China
| | - Zhi Li
- College of Forestry, Guizhou University, Guiyang, China.
- Bioaffiliationersity and Nature Conservation Research Center, Guizhou University, Guiyang, China.
| | - Xu Xiao
- College of Forestry, Guizhou University, Guiyang, China
| | - Mingtai An
- College of Forestry, Guizhou University, Guiyang, China
- Bioaffiliationersity and Nature Conservation Research Center, Guizhou University, Guiyang, China
| | - Chao Yan
- College of Forestry, Guizhou University, Guiyang, China
| |
Collapse
|
6
|
Yan R, Gu L, Qu L, Wang X, Hu G. New Insights into Phylogenetic Relationship of Hydrocotyle (Araliaceae) Based on Plastid Genomes. Int J Mol Sci 2023; 24:16629. [PMID: 38068952 PMCID: PMC10706649 DOI: 10.3390/ijms242316629] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Hydrocotyle, belonging to the Hydrocotyloideae of Araliaceae, consists of 95 perennial and 35 annual species. Due to the lack of stable diagnostic morphological characteristics and high-resolution molecular markers, the phylogenetic relationships of Hydrocotyle need to be further investigated. In this study, we newly sequenced and assembled 13 whole plastid genomes of Hydrocotyle and performed comparative plastid genomic analyses with four previously published Hydrocotyle plastomes and phylogenomic analyses within Araliaceae. The plastid genomes of Hydrocotyle exhibited typical quadripartite structures with lengths from 152,659 bp to 153,669 bp, comprising a large single-copy (LSC) region (83,958-84,792 bp), a small single-copy (SSC) region (18,585-18,768 bp), and a pair of inverted repeats (IRs) (25,058-25,145 bp). Each plastome encoded 113 unique genes, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Comparative analyses showed that the IR boundaries of Hydrocotyle plastomes were highly similar, and the coding and IR regions exhibited more conserved than non-coding and single-copy (SC) regions. A total of 2932 simple sequence repeats and 520 long sequence repeats were identified, with specificity in the number and distribution of repeat sequences. Six hypervariable regions were screened from the SC region, including four intergenic spacers (IGS) (ycf3-trnS, trnS-rps4, petA-psbJ, and ndhF-rpl32) and two coding genes (rpl16 and ycf1). Three protein-coding genes (atpE, rpl16, and ycf2) were subjected to positive selection only in a few species, implying that most protein-coding genes were relatively conserved during the plastid evolutionary process. Plastid phylogenomic analyses supported the treatment of Hydrocotyle from Apiaceae to Araliaceae, and topologies with a high resolution indicated that plastome data can be further used in the comprehensive phylogenetic research of Hydrocotyle. The diagnostic characteristics currently used in Hydrocotyle may not accurately reflect the phylogenetic relationships of this genus, and new taxonomic characteristics may need to be evaluated and selected in combination with more comprehensive molecular phylogenetic results.
Collapse
Affiliation(s)
- Rongrong Yan
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Li Gu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Lu Qu
- Institute of Medicinal Plant Development Yunnan Branch, Chinese Academy of Medical Sciences, Jinghong 666100, China;
| | - Xiaoyu Wang
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Guoxiong Hu
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (R.Y.); (L.G.); (X.W.)
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| |
Collapse
|
7
|
Chen X, Li B, Zhang X. Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis. Sci Rep 2023; 13:18731. [PMID: 37907468 PMCID: PMC10618267 DOI: 10.1038/s41598-023-45421-8] [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: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.
Collapse
Affiliation(s)
- Xiaoli Chen
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Buyu Li
- College of Life Sciences, China West Normal University, Nanchong, 637009, China
| | - Xuemei Zhang
- College of Life Sciences, China West Normal University, Nanchong, 637009, China.
| |
Collapse
|
8
|
Kousar M, Park J. Comparative Analysis of the Chloroplast Genome of Sicyos angulatus with Other Seven Species of Cucurbitaceae Family. Genes (Basel) 2023; 14:1776. [PMID: 37761916 PMCID: PMC10531474 DOI: 10.3390/genes14091776] [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: 06/26/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Sicyos angulatus (SA) is an annual plant from the Cucurbitaceae family that is native to the eastern part of North America. This study aims to assemble and annotate the chloroplast genome of S. angulatus, and then compare it with plastomes of the other species representing the Cucurbitaceae family. The chloroplast genome size of S. angulatus is 154,986 bp, including a pair of inverted repeats (IR) of 26,276 bp, and small single-copy region (SSC) of 18,079 bp and large single-copy region (LSC) of 84,355 bp. Compared to other Cucurbitaceae species, the chloroplast genome of S. angulatus is almost 4222 bp smaller than the plastome Gynostemma pentaphyllum. All other seven species have an identical set of tRNA (37), except Citrullus laevigata, which contains 36 tRNA. The IRa/LSC junction in all eight species is located upstream of rpl2 and downstream of trnH gene. Moreover, variation in the size of the gene and the presence of pseudogene ycf1 has been seen because of the IR contraction and expansion. The highest number of tandem repeats was seen in G. pentaphyllum, and then Corynocarpus leavigata. The sequence divergence analysis and topology of the phylogenetic tree indicate that S. angulatus is more similar to genus Citrullus as compared to genus Gynostemma. These findings contribute to developing the genomic marker for the purpose of future genetic studies.
Collapse
Affiliation(s)
| | - Joonho Park
- Department of Fine Chemistry, Seoul National University of Science and Technology, 232-Gongneung-ro, Nowon-gu, Seoul 01811, Republic of Korea
| |
Collapse
|
9
|
Varilla González JD, Macedo Alves F, Bagnatori Sartori ÂL, de Oliveira Arruda RDC. Diversity and evolution of leaflet anatomical characters in the Pterocarpus clade (Fabaceae: Papilionoideae). J Plant Res 2023; 136:453-481. [PMID: 37029839 DOI: 10.1007/s10265-023-01450-y] [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] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/12/2023] [Indexed: 06/09/2023]
Abstract
The Pterocarpus clade includes 23 genera previously attributed to different Fabaceae tribes. The recent rearrangements of many genera in the clade do not recognize morphological synapomorphies. This study aimed to identify new synapomorphies for the Pterocarpus clade, to identify characters supporting inter-generic relationships currently resolved only by molecular data and to identify diagnostic characters at the genus and species levels. Subterminal leaflets of the studied genera were selected and analyzed using light and scanning electron microscopy. Ancestral reconstruction was performed using morphological and anatomical characters of 16 genera of the Pterocarpus clade. The convex epidermal relief in the region of the main vein indicated the relationship among all genera of the group. Anchor-like multicellular trichomes are features shared by Brya and Cranocarpus, which are the sister group to the other genera of the clade. Subepidermal layers are features shared by the Centrolobium, Etaballia, Paramachaerium, Pterocarpus and Tipuana genera, and the sclerenchyma sheath in the leaflet margin is reported in the Discolobium, Riedeliella and Platymiscium genera. Bulbous based glandular trichomes and vesicular glandular trichomes are diagnostic at the species level in Centrolobium and Pterocarpus, respectively. The leaflet characters investigated can be useful for the taxonomic delimitation at both the genus and species levels of the Pterocarpus clade. Our dataset provides new synapomorphies, elucidates the inter-generic relationships and reinforces the phylogenetic classification of the Pterocarpus clade resolved by molecular data.
Collapse
Affiliation(s)
- Jean David Varilla González
- Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul (UFMS), Avenida Costa e Silva, S/nº, Bairro Universitário, Campo Grande, MS, CEP 79070-900, Brasil
| | - Flávio Macedo Alves
- Laboratório de Sistemática Vegetal, Instituto de Biociências, UFMS, Avenida Costa e Silva, S/nº, Bairro Universitário, Campo Grande, MS, CEP 79070-900, Brasil
| | - Ângela Lúcia Bagnatori Sartori
- Laboratório de Sistemática Vegetal, Instituto de Biociências, UFMS, Avenida Costa e Silva, S/nº, Bairro Universitário, Campo Grande, MS, CEP 79070-900, Brasil.
| | - Rosani do Carmo de Oliveira Arruda
- Laboratório de Anatomia Vegetal, Instituto de Biociências, UFMS, Avenida Costa e Silva, S/nº, Bairro Universitário, Campo Grande, MS, CEP 79070-900, Brasil
| |
Collapse
|
10
|
Gao Y, Li S, Yuan G, Fang J, Shen G, Tian Z. Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae). Biology (Basel) 2023; 12:936. [PMID: 37508367 PMCID: PMC10375975 DOI: 10.3390/biology12070936] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023]
Abstract
Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.
Collapse
Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Shenghui Li
- College of Agriculture, Anshun University, Anshun 561000, China
| | - Guohui Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiapeng Fang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| |
Collapse
|
11
|
Ghosh Dasgupta M, Senthilkumar S, Muthulakshmi E, Balasubramanian A. The draft genome reveals early duplication event in Pterocarpus santalinus: an endemic timber species. Planta 2023; 258:27. [PMID: 37358820 DOI: 10.1007/s00425-023-04190-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION A 541 Mb draft genome of Pterocarpus santalinus is presented and evidence of whole-genome duplication in the Eocene period with expansion of drought responsive gene families is documented. Pterocarpus santalinus Linn. f., popularly known as Red Sanders, is a deciduous tree, endemic to southern parts of Eastern Ghats in India. The heartwood is highly valued in the international market due to its deep red colour, fragrant heartwood and wavy grained texture. In the present study, a high-quality draft genome of P. santalinus was assembled using short and long reads generated from Illumina and Oxford Nanopore Sequencing platforms, respectively. The haploid genome size was estimated at 541 Mb and the hybrid assembly showed 99.60% genome completeness. A total of 51,713 consensus gene set were predicted with 31,437 annotated genes. The age of the whole-genome duplication event in the species was dated at 30-39 mya with 95% confidence suggesting early genome duplication event during the Eocene period. Concurrently, phylogenomic assessment of seven Papilionoideae members including P. santalinus grouped the species based on the tribal classification and established divergence of the tribe Dalbergieae from tribe Trifolieae at ~ 54.20 mya. A significant expansion of water deprivation/drought responsive gene families documented in the study probably explains the occurrence of the species in dry rocky patches. Additionally, re-sequencing of six diverse genotypes predicted one variant every 27 bases. This report presents the first draft genome in the genus Pterocarpus and the unprecedented genomic information generated is expected to accelerate population divergence studies in the species in relation to its endemic nature, support trait-based breeding programme and aid in development of diagnostic tools for timber forensics.
Collapse
Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India.
| | - Shanmugavel Senthilkumar
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
| | - Eswaran Muthulakshmi
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
| | - Aiyar Balasubramanian
- Division of Plant Biotechnology and Cytogenetics, ICFRE-Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, Tamil Nadu, India
| |
Collapse
|
12
|
Xu Q, Li Z, Wu N, Yang J, Yuan L, Zhao T, Sima Y, Xu T. Comparitive Analysis of the Chloroplast Genomes of Three Houpoea Plants. Genes (Basel) 2023; 14:1262. [PMID: 37372442 DOI: 10.3390/genes14061262] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/04/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The genus Houpoea belongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species of Houpoea: Houpoea officinalis var officinalis (OO), Houpoea officinalis var. biloba (OB), and Houpoea rostrata (R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these three Houpoea plants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the three Houpoea plants, it is highly conservative, with only changes between H. rostrata and the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label for Houpoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates that Houpoea is a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties of H. officinalis var. officinalis, H. rostrata, H. officinalis var. biloba, Houpoea obovate, and Houpoea tripetala, which evolved and differentiated from the ancestors of Houpoea to the present Houpoea in the above order. This study provides valuable information on the genus Houpoea, enriches the CPG information on Houpoea genus, and provides genetic resources for the further classification of and phylogenetic research on Houpoea.
Collapse
Affiliation(s)
- Qinbin Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Zhuoran Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Yongkang Sima
- Kunming Arboretum, Yunnan Academy of Forestry & Grassland Science, Kunming 650201, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| |
Collapse
|
13
|
Bi D, Han S, Zhou J, Zhao M, Zhang S, Kan X. Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale. Genes (Basel) 2023; 14:genes14030694. [PMID: 36980966 PMCID: PMC10048229 DOI: 10.3390/genes14030694] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.
Collapse
Affiliation(s)
- De Bi
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Jun Zhou
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Maojin Zhao
- Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Correspondence: ; Tel.: +86-139-5537-2268
| |
Collapse
|
14
|
Mao J, Liang Y, Wang X, Zhang D. Comparison of plastid genomes and ITS of two sister species in Gentiana and a discussion on potential threats for the endangered species from hybridization. BMC Plant Biol 2023; 23:101. [PMID: 36800941 PMCID: PMC9940437 DOI: 10.1186/s12870-023-04088-z] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gentiana rigescens Franchet is an endangered medicinal herb from the family Gentianaceae with medicinal values. Gentiana cephalantha Franchet is a sister species to G. rigescens possessing similar morphology and wider distribution. To explore the phylogeny of the two species and reveal potential hybridization, we adopted next-generation sequencing technology to acquire their complete chloroplast genomes from sympatric and allopatric distributions, as along with Sanger sequencing to produce the nrDNA ITS sequences. RESULTS The plastid genomes were highly similar between G. rigescens and G. cephalantha. The lengths of the genomes ranged from 146,795 to 147,001 bp in G. rigescens and from 146,856 to 147,016 bp in G. cephalantha. All genomes consisted of 116 genes, including 78 protein-coding genes, 30 tRNA genes, four rRNA genes and four pseudogenes. The total length of the ITS sequence was 626 bp, including six informative sites. Heterozygotes occurred intensively in individuals from sympatric distribution. Phylogenetic analysis was performed based on chloroplast genomes, coding sequences (CDS), hypervariable sequences (HVR), and nrDNA ITS. Analysis based on all the datasets showed that G. rigescens and G. cephalantha formed a monophyly. The two species were well separated in phylogenetic trees using ITS, except for potential hybrids, but were mixed based on plastid genomes. This study supports that G. rigescens and G. cephalantha are closely related, but independent species. However, hybridization was confirmed to occur frequently between G. rigescens and G. cephalantha in sympatric distribution owing to the lack of stable reproductive barriers. Asymmetric introgression, along with hybridization and backcrossing, may probably lead to genetic swamping and even extinction of G. rigescens. CONCLUSION G. rigescens and G. cephalantha are recently diverged species which might not have undergone stable post-zygotic isolation. Though plastid genome shows obvious advantage in exploring phylogenetic relationships of some complicated genera, the intrinsic phylogeny was not revealed because of matrilineal inheritance here; nuclear genomes or regions are hence crucial for uncovering the truth. As an endangered species, G. rigescens faces serious threats from both natural hybridization and human activities; therefore, a balance between conservation and utilization of the species is extremely critical in formulating conservation strategies.
Collapse
Affiliation(s)
- Jiuyang Mao
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Yuze Liang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Xue Wang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, 671000, Yunnan, China.
- Yunnan Key Laboratory of Screening and Research on Anti-pathogenic Plant Resources from Western Yunnan (Cultivation), Dali, 671000, Yunnan, China.
| |
Collapse
|
15
|
Du S, Hu X, Guo Y, Wang S, Yang X, Wu Z, Huang Y. A comparative plastomic analysis of Ziziphus jujuba var. spinosa (Bunge) Hu ex H. F. Chow and implication of the origin of Chinese jujube. AoB Plants 2023; 15:plad006. [PMID: 37025103 PMCID: PMC10071050 DOI: 10.1093/aobpla/plad006] [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: 08/25/2022] [Accepted: 02/17/2023] [Indexed: 06/19/2023]
Abstract
Comparative plastomics can be used to explicitly dissect various types of plastome variation. In the present study, the plastome variation pattern of Ziziphus jujuba var. spinosa (also called sour jujube) and its phylogenomic relationship with Chinese jujube were investigated. Plastomes of 21 sour jujube individuals were sequenced and assembled. The length of the sour jujube plastomes ranged between 159399 and 161279 bp. The plastomes exhibited collinearity of structure, gene order and content. The most divergent regions were located in the intergenic spacers, such as trnR-UCU-atpA and psbZ-trnG-UCC. Sliding window analysis demonstrated that the sequence variation among the sour jujube plastomes was relatively low. Sixty-two to 76 SSRs with 4 motif types were identified in the sour jujube plastomes with a predominant motif type of A/T. Three protein-coding genes exhibited higher nonsynonymous/synonymous substitution ratios, indicating that these genes may undergo positive selection. A total of 80 SNPs were detected and 1266 potential RNA editing sites of 23 protein-coding genes were predicted. In the phylogenomic tree constructed, sour jujube has a sister relationship to Chinese jujube, which indicates that Chinese jujube may have originated or been domesticated from sour jujube. The present study explicitly investigated the individual-level plastome variation of sour jujube and provides potential valuable molecular markers for future genetic-related study of this lineage.
Collapse
Affiliation(s)
- Shuhui Du
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaoyan Hu
- College of Food Science and Technology, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yuanting Guo
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shengji Wang
- College of Forestry, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhenzhen Wu
- Taian Dushihuaxiang Agricultural Technology Co., Ltd, Taian, Shandong, China
| | - Yuyin Huang
- Shandong Huinongtianxia Science and Technology Information Consulting Co., Ltd, Taian, Shandong, China
| |
Collapse
|
16
|
Hu Q, Qian R, Zhang Y, Ma X, Ye Y, Zhang X, Lin L, Liu H, Zheng J. Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China. Sci Rep 2023; 13:1356. [PMID: 36693990 PMCID: PMC9873718 DOI: 10.1038/s41598-023-28432-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Sphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.
Collapse
Affiliation(s)
- Qingdi Hu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Renjuan Qian
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Yanjun Zhang
- China National Bamboo Research Center, Hangzhou, 310012, Zhejiang, China
| | - Xiaohua Ma
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Youju Ye
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Xule Zhang
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Lin Lin
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Hongjian Liu
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China
| | - Jian Zheng
- Wenzhou Key Laboratory of Resource Plant Innovation and Utilization, Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, Zhejiang, China.
| |
Collapse
|
17
|
Jiang D, Cai X, Gong M, Xia M, Xing H, Dong S, Tian S, Li J, Lin J, Liu Y, Li HL. Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae). BMC Genomics 2023; 24:30. [PMID: 36653780 PMCID: PMC9848714 DOI: 10.1186/s12864-023-09115-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. RESULTS We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. CONCLUSIONS This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.
Collapse
Affiliation(s)
- Dongzhu Jiang
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Xiaodong Cai
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Min Gong
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Maoqin Xia
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Haitao Xing
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Shanshan Dong
- grid.9227.e0000000119573309Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Shuming Tian
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.411581.80000 0004 1790 0881College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, 404100 China
| | - Jialin Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Junyao Lin
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| | - Yiqing Liu
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China ,grid.410654.20000 0000 8880 6009College of Horticulture and Gardening, Yangtze University, Jingzhou, 433200 China
| | - Hong-Lei Li
- grid.449955.00000 0004 1762 504XCollege of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Yongchuan, 402160 China
| |
Collapse
|
18
|
Gao Y, Shen G, Yuan G, Tian Z. Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields. Int J Mol Sci 2022; 23:ijms232213864. [PMID: 36430336 PMCID: PMC9698722 DOI: 10.3390/ijms232213864] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/30/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.
Collapse
|
19
|
Xie H, Zhang L, Zhang C, Chang H, Xi Z, Xu X. Comparative analysis of the complete chloroplast genomes of six threatened subgenus Gynopodium (Magnolia) species. BMC Genomics 2022; 23:716. [PMID: 36261795 PMCID: PMC9583488 DOI: 10.1186/s12864-022-08934-6] [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: 04/06/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The subgenus Gynopodium belonging to genus Magnolia have high ornamental, economic, and ecological value. Subgenus Gynopodium contains eight species, but six of these species are threatened. No studies to date have characterized the characteristics of the chloroplast genomes (CPGs) within subgenus Gynopodium species. In this study, we compared the structure of CPGs, identified the mutational hotspots and resolved the phylogenetic relationship of subgenus Gynopodium. RESULTS The CPGs of six subgenus Gynopodium species ranged in size from 160,027 bp to 160,114 bp. A total of 131 genes were identified, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. We detected neither major expansions or contractions in the inverted repeat region, nor rearrangements or insertions in the CPGs of six subgenus Gynopodium species. A total of 300 large repeat sequences (forward, reverse, and palindrome repeats), 847 simple sequence repeats, and five highly variable regions were identified. One gene (ycf1) and four intergenic regions (psbA-trnH-GUG, petA-psbJ, rpl32-trnL-UAG, and ccsA-ndhD) were identified as mutational hotspots by their high nucleotide diversity (Pi) values (≥ 0.004), which were useful for species discrimination. Maximum likelihood and Bayesian inference trees were concordant and indicated that Magnoliaceae consisted of two genera Liriodendron and Magnolia. Six species of subgenus Gynopodium clustered as a monophyletic clade, forming a sister clade with subgenus Yulania (BS = 100%, PP = 1.00). Due to the non-monophyly of subgenus Magnolia, subgenus Gynopodium should be treated as a section of Magnolia. Within section Gynopodium, M. sinica diverged first (posterior probability = 1, bootstrap = 100), followed by M. nitida, M. kachirachirai and M. lotungensis. M. omeiensis was sister to M. yunnanensis (posterior probability = 0.97, bootstrap = 50). CONCLUSION The CPGs and characteristics information provided by our study could be useful in species identification, conservation genetics and resolving phylogenetic relationships of Magnoliaceae species.
Collapse
Affiliation(s)
- Huanhuan Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, China
| | - Cheng Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Hong Chang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Han S, Wang R, Hong X, Wu C, Zhang S, Kan X. Plastomes of Bletilla (Orchidaceae) and Phylogenetic Implications. Int J Mol Sci 2022; 23:ijms231710151. [PMID: 36077549 PMCID: PMC9456473 DOI: 10.3390/ijms231710151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 07/30/2022] [Revised: 08/22/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The genus Bletilla is a small genus of only five species distributed across Asia, including B. chartacea, B. foliosa, B. formosana, B. ochracea and B. striata, which is of great medicinal importance. Furthermore, this genus is a member of the key tribe Arethuseae (Orchidaceae), harboring an extremely complicated taxonomic history. Recently, the monophyletic status of Bletilla has been challenged, and the phylogenetic relationships within this genus are still unclear. The plastome, which is rich in both sequence and structural variation, has emerged as a powerful tool for understanding plant evolution. Along with four new plastomes, this work is committed to exploring plastomic markers to elucidate the phylogeny of Bletilla. Our results reveal considerable plastomic differences between B. sinensis and the other three taxa in many aspects. Most importantly, the specific features of the IR junction patterns, novel pttRNA structures and codon aversion motifs can serve as useful molecular markers for Bletilla phylogeny. Moreover, based on maximum likelihood and Bayesian inference methods, our phylogenetic analyses based on two datasets of Arethuseae strongly imply that Bletilla is non-monophyletic. Accordingly, our findings from this study provide novel potential markers for species identification, and shed light on the evolution of Bletilla and Arethuseae.
Collapse
Affiliation(s)
- Shiyun Han
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
| | - Rongbin Wang
- Institute of Chinese Medicine Resources, Anhui College of Traditional Chinese Medicine, Wuhu 241002, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xin Hong
- Anhui Provincial Engineering Laboratory of Wetland Ecosystem Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Cuilian Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Sijia Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xianzhao Kan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, Wuhu 241000, China
- Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Correspondence: ; Tel.: +86-139-5537-2268
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Contreras-Díaz R, Carevic FS, Huanca-Mamani W, Oses R, Arias-Aburto M, Navarrete-Fuentes M. Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
24
|
Li C, Liu Y, Lin F, Zheng Y, Huang P. Characterization of the complete chloroplast genome sequences of six Dalbergia species and its comparative analysis in the subfamily of Papilionoideae (Fabaceae). PeerJ 2022; 10:e13570. [PMID: 35795179 PMCID: PMC9252178 DOI: 10.7717/peerj.13570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/19/2021] [Accepted: 05/20/2022] [Indexed: 01/17/2023] Open
Abstract
Dalbergia spp. are numerous and widely distributed in pantropical areas in Asia, Africa and America, and most of the species have important economic and ecological value as precious timber. In this study, we determined and characterized six complete chloroplast genomes of Dalbergia species (Dalbergia obtusifolia, D. hupeana, D. mimosoides, D. sissoo, D. hancei, D. balansae), which displayed the typical quadripartite structure of angiosperms. The sizes of the genomes ranged from 155,698 bp (D. hancei) to 156,419 bp (D. obtusifolia). The complete chloroplast genomes of Dalbergia include 37 tRNA genes, eight rRNA genes and 84 protein-coding genes. We analysed the sequence diversity of Dalberigia chloroplast genomes coupled with previous reports. The results showed 12 noncoding regions (rps16-accD, trnR-UCU-trnG-UCC, ndhE-ndhG, trnG-UCC-psbZ, rps8-rpl14, trnP-UGG-psaJ, ndhH-rps15, trnQ-UUG-rps16, trnS-GCU-psbI, rps12-clpP, psbA-trnK-UUU, trnK-UUU-intron), and four coding regions (rps16, ycf1, rps15 and ndhF) showed many nucleotide variations that could be used as potential molecular markers. Based on a site-specific model, we analysed the selective pressure of chloroplast genes in Dalbergia species. Twenty-two genes with positively selected sites were detected, involving the photosynthetic system (ndhC, adhD, ndhF, petB, psaA, psaB, psbB, psbC, psbK and rbcL), self-replication category of genes (rpoA, rpoC2, rps3, rps12 and rps18) and others (accD, ccsA, cemA, clpP, matK, ycf1 and ycf2). Additionally, we identified potential RNA editing sites that were relatively conserved in the genus Dalbergia. Furthermore, the comparative analysis of cp genomes of Dalbergieae species indicated that the boundary of IRs/SSC was highly variable, which resulted in the size variation of cp genomes. Finally, phylogenetic analysis showed an inferred phylogenetic tree of Papilionoideae species with high bootstrap support and suggested that Amorpheae was the sister of the clade Dalbergieae. Moreover, three genera of the Pterocarpus clade showed a nested evolutionary relationship. These complete cp genomes provided valuable information for understanding the genetic variation and phylogenetic relationship of Dalbergia species with their relatives.
Collapse
Affiliation(s)
- Changhong Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yu Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Wenzhou, Zhejiang, China
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
25
|
Xia X, Peng J, Yang L, Zhao X, Duan A, Wang D. Comparative Analysis of the Complete Chloroplast Genomes of Eight Ficus Species and Insights into the Phylogenetic Relationships of Ficus. Life (Basel) 2022; 12:life12060848. [PMID: 35743879 PMCID: PMC9224849 DOI: 10.3390/life12060848] [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: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/30/2022] Open
Abstract
The genus Ficus is an evergreen plant, the most numerous species in the family Moraceae, and is often used as a food and pharmacy source. The phylogenetic relationships of the genus Ficus have been debated for many years due to the overlapping phenotypic characters and morphological similarities between the genera. In this study, the eight Ficus species (Ficus altissima, Ficus auriculata, Ficus benjamina, Ficus curtipes, Ficus heteromorpha, Ficus lyrata, Ficus microcarpa, and Ficus virens) complete chloroplast (cp) genomes were successfully sequenced and phylogenetic analyses were made with other Ficus species. The result showed that the eight Ficus cp genomes ranged from 160,333 bp (F. heteromorpha) to 160,772 bp (F. curtipes), with a typical quadripartite structure. It was found that the eight Ficus cp genomes had similar genome structures, containing 127 unique genes. The cp genomes of the eight Ficus species contained 89−104 SSR loci, which were dominated by mono-nucleotides repeats. Moreover, we identified eight hypervariable regions (trnS-GCU_trnG-UCC, trnT-GGU_psbD, trnV-UAC_trnM-CAU, clpP_psbB, ndhF_trnL-UAG, trnL-UAG_ccsA, ndhD_psaC, and ycf1). Phylogenetic analyses have shown that the subgenus Ficus and subgenus Synoecia exhibit close affinities and based on the results, we prefer to merge the subgenus Synoecia into the subgenus Ficus. At the same time, new insights into the subgeneric classification of the Ficus macrophylla were provided. Overall, these results provide useful data for further studies on the molecular identification, phylogeny, species identification and population genetics of speciation in the Ficus genus.
Collapse
Affiliation(s)
- Xi Xia
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Jingyu Peng
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100089, China;
| | - Lin Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Xueli Zhao
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Anan Duan
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
| | - Dawei Wang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, College of Forestry, Southwest Forestry University, Kunming 650224, China; (X.X.); (L.Y.); (X.Z.); (A.D.)
- Correspondence: ; Tel.: +86-138-8891-5161
| |
Collapse
|
26
|
Zhou T, Ning K, Mo Z, Zhang F, Zhou Y, Chong X, Zhang D, El-Kassaby YA, Bian J, Chen H. Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae. PLoS One 2022; 17:e0268679. [PMID: 35588136 PMCID: PMC9119449 DOI: 10.1371/journal.pone.0268679] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.
Collapse
Affiliation(s)
- Ting Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Kun Ning
- College of Horticulture, Jinling Institute of Technology, Nanjing City, Jiangsu Province, P.R. China
| | - Zhenghai Mo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Fan Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Yanwei Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinran Chong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Donglin Zhang
- Department of Horticulture, University of Georgia, Athens, GA, United States of America
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jian Bian
- Jiangsu Yufeng Tourism Development Co. Ltd., Yancheng, China
| | - Hong Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
- * E-mail:
| |
Collapse
|
27
|
Fan X, Wang W, Wagutu GK, Li W, Li X, Chen Y. Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships. BMC Plant Biol 2022; 22:230. [PMID: 35513783 PMCID: PMC9069798 DOI: 10.1186/s12870-022-03608-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 06/27/2021] [Accepted: 04/19/2022] [Indexed: 05/06/2023]
Abstract
BACKGROUND Trapa L. is a floating-leaved aquatic plant with important economic and ecological values. However, the species identification and phylogenetic relationship within Trapa are still controversial, which necessitates the need for plastid genome information of Trapa. In this study, complete chloroplast genomes of 13 Trapa species/taxa were sequenced and annotated. Combined with released sequences, comparative analyses of chloroplast genomes were performed on the 15 Trapa species/taxa for the first time. RESULTS The Trapa chloroplast genomes exhibited typical quadripartite structures with lengths from 155,453 to 155,559 bp. The gene orders and contents within Trapa were conservative, but several changes were found in the microstructure. The intron loss of rpl2, also detected in Lythraceae, was found in all Trapa species/taxa, suggesting close genetic relationship between Lythraceae and Trapaceae. Notably, two small-seed species (T. incisa and T. maximowiczii) showed the smallest genome size with 155,453 and 155,477 bp, respectively. Each cp genome contained the same 130 genes consisting of 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Trapa species/taxa showed 37 (T. incisa and T. maximowiczii) to 41 (T. sibirica) long repeats, including forward, palindromic, reversed and complementary repeats. There were 110 (T. quadrispinosa) to 123 (T. incisa and T. maximowiczii) SSR (simple sequence repeat) loci in Trapa chloroplast genomes. Comparative analyses revealed that two hotspot regions (atpA-atpF and rps2-rpoC2) in Trapa chloroplast genomes could be served as potential molecular markers. Three phylogenetic analyses (ML, MP and BI) consistently showed that there were two clusters within Trapa, including large- and small-seed species/taxa, respectively; for the large-seed Trapa, they clustered according to their geographical origin and tubercle morphology on the surface of seeds. CONCLUSION In summary, we have acquired the sequences of 13 Trapa chloroplast genomes, and performed the comparative analyses within Trapa for the first time. The results have helped us better identify the Trapa species/taxa and deepen the understanding of genetic basis and phylogenetic relationship of Trapa, which will facilitate the effective management and utilization of the important genetic resources in the future.
Collapse
Affiliation(s)
- Xiangrong Fan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- College of Science, Tibet University, Lhasa, 850000, People's Republic of China
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, 850000, People's Republic of China
| | - Wuchao Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Godfrey K Wagutu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Wei Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Xiuling Li
- College of Life Science, Linyi University, Linyi, 276000, People's Republic of China.
| | - Yuanyuan Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
| |
Collapse
|
28
|
Tang D, Lin Y, Wei F, Quan C, Wei K, Wei Y, Cai Z, Kashif MH, Miao J. Characteristics and comparative analysis of Mesona chinensis Benth chloroplast genome reveals DNA barcode regions for species identification. Funct Integr Genomics 2022; 22:467-479. [PMID: 35318559 DOI: 10.1007/s10142-022-00846-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022]
Abstract
Mesona chinensis Benth (MCB) is an important medicinal and edible plant in Southern China and Southeast Asian countries. Chloroplast (cp) genome is usually used for plant phylogeny, species identification, and chloroplast genetic engineering. To characterize the cp genome and determine the evolutionary position and perform the genetic diversity analysis of MCB, we sequence and characterize the MCB cp genome. The results show that the cp genome of MCB is a single circular molecule with a length of 152,635 bp. It is a typical quadripartite structure, comprising a large single-copy region (LSC, 83,514 bp) and a small single-copy region (SSC, 17,751 bp) separated by two inverted repeat regions (IRs, 51,370 bp). It encodes 129 unique genes, including 84 protein-coding genes (PCGs), 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Altogether 127 simple sequence repeats (SSRs) are identified in the MCB cp genome with 86.61% of mononucleotide repeats. Phylogenetic analysis reveals that MCB is most closely related to Ocimum basilicum based on the whole cp genomes. Several highly divergent regions are found, such as trnH_psbA, rps16_trnQ, trnS_trnG, trnE_trnT, psaA_ycf3, rpl32_trnL, ccsA_ndhD, ndhG_ndhI, and rps15_ycf1, which can be proposed for use as DNA barcode regions. Genetic diversity analysis unveils a relatively narrow genetic basis of MCB germplasm resources. Therefore, the innovative breeding of MCB is very urgent and necessary in future research.
Collapse
Affiliation(s)
- Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China. .,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Yang Lin
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Changqian Quan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Kunhua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Yanyan Wei
- College of Agriculture, Guangxi University, Nanning, China
| | - Zhongquan Cai
- College of Agriculture, Guangxi University, Nanning, China
| | | | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China. .,Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| |
Collapse
|
29
|
Wang L, Liu B, Yang Y, Zhuang Q, Chen S, Liu Y, Huang S. The comparative studies of complete chloroplast genomes in Actinidia (Actinidiaceae): novel insights into heterogenous variation, clpP gene annotation and phylogenetic relationships. Mol Genet Genomics 2022. [PMID: 35175427 DOI: 10.1007/s00438-022-01868-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/30/2022] [Indexed: 10/19/2022]
Abstract
The genus Actinidia, also called kiwifruit, is characterized with abundant balanced nutritional metabolites, including exceptionally high vitamin C content. However, the traditional classification could not fully reflect the actual Actinidia species' relationships, which need further revision through more accurate approaches. Compared to the nuclear genome, the chloroplast genome has simple heredity characteristics, conserved genome structure and small size, suitable for deciphering complicated species' phylogenetic relationships. Here, the genome-wide comprehensive comparative analyses were performed over 29 independent chloroplast genomes' sequences derived from 25 Actinidia taxa. The average genome size is 156,673.38 bp, with an average 37.20% GC content. The long repeat sequences rather than SSRs (simple sequence repeats) in Actinidia were revealed to be the causal agent leading to the chloroplast genome size expansion. The clpP gene sequences with exon merge and intron deletion were annotated in all the 29 chloroplast genomes tested, which has been previously reported to be lost in Actinidia species. Comprehensive sequence analyses indicated the distinct variation at the clpP gene locus was Actinidiaceae-specific, emerging after the Actinidiaceae-other Ericales species divergence. Four highly divergent sequences (i.e., rps16 ~ trnQ-UUG, rps4 ~ trnT-UGU, petA ~ psbJ, and rps12 ~ psbB) evolved in the LSC (large single-copy) and SSC (small single-copy) regions embodying rps12 ~ psbB (including clpP gene and its up/downstream noncoding sequence) were identified as variation hot spots in Actinidia species. Based on either LSC region alone, combined sequences of LSC and SSC or the whole chloroplast genome sequences, three identical phylogenetic trees of the 25 Actinidia taxa with relatively improved resolution were reconstructed, consistently supporting the reticulate evolutionary lineage in Actinidia. Our findings could help to better understand the evolution characteristics of chloroplast genomes and phylogenetic relationships among Actinidia species.
Collapse
|
30
|
Liang D, Wang H, Zhang J, Zhao Y, Wu F. Complete Chloroplast Genome Sequence of Fagus longipetiolata Seemen (Fagaceae): Genome Structure, Adaptive Evolution, and Phylogenetic Relationships. Life (Basel) 2022; 12:92. [PMID: 35054485 DOI: 10.3390/life12010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/26/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023]
Abstract
Fagus longipetiolata Seemen is a deciduous tree of the Fagus genus in Fagaceae, which is endemic to China. In this study, we successfully sequenced the cp genome of F. longipetiolata, compared the cp genomes of the Fagus genus, and reconstructed the phylogeny of Fagaceae. The results showed that the cp genome of F. longipetiolata was 158,350 bp, including a pair of inverted repeat (IRA and IRB) regions with a length of 25,894 bp each, a large single-copy (LSC) region of 87,671 bp, and a small single-copy (SSC) region of 18,891 bp. The genome encoded 131 unique genes, including 81 protein-coding genes, 37 transfer RNA genes (tRNAs), 8 ribosomal RNA genes (rRNAs), and 5 pseudogenes. In addition, 33 codons and 258 simple sequence repeats (SSRs) were identified. The cp genomes of Fagus were relatively conserved, especially the IR regions, which showed the best conservation, and no inversions or rearrangements were found. The five regions with the largest variations were the rps12, rpl32, ccsA, trnW-CCA, and rps3 genes, which spread over in LSC and SSC. The comparison of gene selection pressure indicated that purifying selection was the main selective pattern maintaining important biological functions in Fagus cp genomes. However, the ndhD, rpoA, and ndhF genes of F. longipetiolata were affected by positive selection. Phylogenetic analysis revealed that F. longipetiolata and F. engleriana formed a close relationship, which partially overlapped in their distribution in China. Our analysis of the cp genome of F. longipetiolata would provide important genetic information for further research into the classification, phylogeny and evolution of Fagus.
Collapse
|
31
|
Yang J, Hu G, Hu G. Comparative genomics and phylogenetic relationships of two endemic and endangered species (Handeliodendron bodinieri and Eurycorymbus cavaleriei) of two monotypic genera within Sapindales. BMC Genomics 2022; 23:27. [PMID: 34991482 PMCID: PMC8734052 DOI: 10.1186/s12864-021-08259-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 08/18/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. RESULTS The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei, and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer, Dipteronia, Aesculus, and Handeliodendron. IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1, ndhC-trnV-UAC, and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa. CONCLUSION This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus.
Collapse
Affiliation(s)
- Jiaxin Yang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Guoxiong Hu
- College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Guangwan Hu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| |
Collapse
|
32
|
Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). Biology (Basel) 2022; 11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.
Collapse
Affiliation(s)
| | | | - Xue-Jie Zhang
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| |
Collapse
|
33
|
Agudelo ID, Aldaco G, Brito-Pizano A, Chavez KG, Cortina KG, Flores J, Fuentes A, Garcia AN, Garcia A, Gonzalez-Martinez D, Hernandez Ramos J, Hughey JR, Katada FR, Leon FA, Lopez MP, Lopez SZ, Mendoza AG, Molina M, Muhrram A, Ortiz-Matias D, Ortiz TE, Pacheco A, Patel N, Ramirez PM, Scaramuzzino JL, Soto A, Stabler RA, Vidauri JM, Villicana J, Yhip JA. The complete chloroplast genome of the threatened Napa False Indigo Amorpha californica var. napensis Jeps. 1925 (Fabaceae) from Northern California, USA. Mitochondrial DNA B Resour 2022; 7:283-285. [PMID: 35111938 PMCID: PMC8803116 DOI: 10.1080/23802359.2022.2029605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
| | - Ivan D. Agudelo
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Griselda Aldaco
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Angel Brito-Pizano
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Kimberly G. Chavez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Karina G. Cortina
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jorge Flores
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alejandro Fuentes
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Adam N. Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alejandro Garcia
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | | | | | - Jeffery R. Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Fernando R. Katada
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Felix A. Leon
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Maleny P. Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Sandra Z. Lopez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Aileen G. Mendoza
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Maritta Molina
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Asmahan Muhrram
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Daisy Ortiz-Matias
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Tonantzin E. Ortiz
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Alicia Pacheco
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Nandini Patel
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Paz M. Ramirez
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | | | - Alexandria Soto
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | | | - Jessica M. Vidauri
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - Jose Villicana
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| | - James A. Yhip
- Division of Mathematics, Science, and Engineering, Hartnell College, Salinas, CA, USA
| |
Collapse
|
34
|
Li DM, Li J, Wang DR, Xu YC, Zhu GF. Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae). BMC Plant Biol 2021; 21:558. [PMID: 34814832 PMCID: PMC8611967 DOI: 10.1186/s12870-021-03315-9] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. RESULTS Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda 'Red Leaf', Kaempferia rotunda 'Silver Diamonds' and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630-163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172-88,632 bp), a small single copy (SSC, 15,393-15,917 bp) and a pair of inverted repeats (IRs, 29,673-29,833 bp). The genomes contain 111-113 different genes, including 79 protein coding genes, 28-30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + "the Kaempferia clade" consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. CONCLUSIONS Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.
Collapse
Affiliation(s)
- Dong-Mei Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Jie Li
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dai-Rong Wang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ye-Chun Xu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| |
Collapse
|
35
|
Zeng S, Li J, Yang Q, Wu Y, Yu J, Pei X, Yu J. Comparative plastid genomics of Mazaceae: focusing on a new recognized genus, Puchiumazus. Planta 2021; 254:99. [PMID: 34665332 DOI: 10.1007/s00425-021-03753-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/16/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Six Mazaceae plastomes were assembled in this study, including the newly recognized genus, Puchiumazus. Comparative plastid genomic analysis provided new insights into Mazaceae. The phylogenetic categorization of Mazus lanceifolius (Mazaceae) has long been uncertain. In 2021, the scholars Bo Li, D. G. Zhang, and C. L. Xiang republished M. lanceifolius as a new species Puchiumazus lanceifolius, within a new genus Puchiumazus. However, there is little plastome information on Mazaceae. Following the publishing of the new genus Puchiumazus, it is now necessary to study the Mazaceae plastome features to comprehensively understand this young family. The Mazaceae plastomes all have a typical quartile structure. The plastomes have a size ranging from 152,388 to 154,252 bp, and each plastome contains 112 unique genes, including 78 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. A comparative analysis showed that these plastome sequences are highly conserved. Furthermore, we identified four relatively hypervariable regions (trnQ-UUC-psbK, trnS-GCU- trnS-CGA, trnT-UGU-trnL-UAA and ycf1) that can be used as potential DNA barcodes for the identification of this clade. Phylogenetic relationships based on the whole plastome sequences of 25 samples of 14 genera of Lamiales placed M. lanceifolius in the basal clade of the family Mazaceae, with 100% bootstrap support. In summary, the M. lanceifolius results indicate that a new monotype genus (Puchiumazus) should be established at the whole-plastome level. This study provides plastid genomic resources for exploring the phylogeny of Mazaceae.
Collapse
Affiliation(s)
- Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Qiyi Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You Wu
- College of Information and Electrical Engineering, Chongqing Three Gorges University, Chongqing, 404199, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Xiaoying Pei
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
| |
Collapse
|
36
|
Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics 2021; 22:672. [PMID: 34536995 PMCID: PMC8449883 DOI: 10.1186/s12864-021-07967-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
Collapse
Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Weidong Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| |
Collapse
|
37
|
Tian C, Li X, Wu Z, Li Z, Hou X, Li FY. Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae). Front Genet 2021; 12:705482. [PMID: 34422006 PMCID: PMC8378255 DOI: 10.3389/fgene.2021.705482] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.
Collapse
Affiliation(s)
- Chunyu Tian
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiansong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zinian Wu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Zhiyong Li
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China.,Key Laboratory of Grassland Resources and Utilization of Ministry of Agriculture, Hohhot, China
| | - Xiangyang Hou
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| |
Collapse
|
38
|
Senthilkumar S, Ulaganathan K, Ghosh Dasgupta M. Reference-based assembly of chloroplast genome from leaf transcriptome data of Pterocarpus santalinus. 3 Biotech 2021; 11:393. [PMID: 34458062 DOI: 10.1007/s13205-021-02943-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/13/2021] [Accepted: 07/25/2021] [Indexed: 12/25/2022] Open
Abstract
Chloroplast genome sequencing is an essential tool to understand genome evolution and phylogenetic relationship. The available methods for constructing chloroplast genome include chloroplast enrichment followed by long overlapping PCR or extraction and assembly of chloroplast-specific reads from whole-genome datasets. In the present study, we propose an alternate strategy of extraction and assembly of chloroplast-specific reads from leaf transcriptome data of Pterocarpus santalinus using bowtie2 aligner program. The assembled genome was compared with the published chloroplast genome of P. santalinus for genome size, number of predicted genes, microsatellite repeat motifs, and nucleotide repeats. A near-complete chloroplast genome was assembled from the transcriptome reads. The proposed method requires less computational time and know-how, limited virtual memory, and is cost-effective when compared to whole-genome sequencing. Assembly of Cp genome from transcriptome data will enhance the resolution of phylogenetic studies through comparative plastome analysis, facilitate accurate species/genotype discrimination and accelerate the development of transplastomic plants with enhanced biotic and abiotic tolerance. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02943-0.
Collapse
Affiliation(s)
- Shanmugavel Senthilkumar
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
| | - Kandasamy Ulaganathan
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, 500007 Andhra Pradesh India
| | - Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, Forest Campus, R.S. Puram, Coimbatore, 641002 Tamil Nadu India
| |
Collapse
|
39
|
Zhang Y, Wang Z, Guo Y, Chen S, Xu X, Wang R. Complete chloroplast genomes of Leptodermis scabrida complex: Comparative genomic analyses and phylogenetic relationships. Gene 2021; 791:145715. [PMID: 33984444 DOI: 10.1016/j.gene.2021.145715] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 08/14/2020] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/16/2022]
Abstract
Leptodermis scabrida complex is one of the important components of genus Leptodermis, which is mainly distributed in the Himalaya Mountains. It includes species of L. gracilis, L. hirsutiflora, L. hirsutiflora var. ciliata, L. kumaonensis, L. pilosa var. acanthoclada and L. scabrida. However, species boundaries and relationships within this complex are unclear based on current morphological and molecular evidence. We sequenced 13 complete chloroplast (cp) genomes representing seven taxa of the complex and two non-Leptodermis scabrida complex taxa. After de novo assembly and annotation, we performed comparative genomic analysis. All cp genomes showed highly conserved structures, and the genome sizes ranged from 154,369 bp to 154,885 bp and possessed the same GC content (37.5%). A total of 113 unique genes were identified in each cp sample, including 79 protein coding genes, 30 tRNAs, and four rRNAs. Repeat sequences and SSRs were detected, showing great similarity among all taxa in this complex. Six highly variable regions, including trnS-trnG, rps2-rpoC2, ndhF, rpl32-ccsA, ccsA-ndhD, and ndhA, were screened as potential molecular markers for phylogenetic reconstruction. Based on a total of 27 complete cp genome sequences, the consistent and robust phylogenetic relationships were firstly constructed and the same species within L. scabrida complex clustered into a group. The divergence time of Leptodermis from ancestral taxa occurred at the middle Eocene, which might be due to geological and climatic changes. The 13 complete cp genome sequences reported will provide new clues for phylogeny elucidation, species identification and evolutionary history speculation of Leptodermis, as well as in Rubiaceae.
Collapse
Affiliation(s)
- Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengfeng Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yanan Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Sheng Chen
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianyi Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ruijiang Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
40
|
Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep 2021; 11:9471. [PMID: 33947883 PMCID: PMC8096831 DOI: 10.1038/s41598-021-88160-4] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 02/02/2023] Open
Abstract
The chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
Collapse
Affiliation(s)
- Jiawei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China
| | - Hongmei Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The Second Peoples's Hospital of Nantong, Nantong, 226000, Jiangsu, China
| | - Bin Ai
- Foshan Green Development Innovation Research Institute, Foshan, 528000, Guangdong, China
| | - Wei Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuijun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qili Fei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhiqiang Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Sen Li
- The College of Horticulture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| |
Collapse
|
41
|
Kong BL, Park HS, Lau TD, Lin Z, Yang TJ, Shaw PC. Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes. Sci Rep 2021; 11:5153. [PMID: 33664414 DOI: 10.1038/s41598-021-84705-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Ilex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.
Collapse
|
42
|
Li J, Tang J, Zeng S, Han F, Yuan J, Yu J. Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea. BMC Plant Biol 2021; 21:25. [PMID: 33413130 PMCID: PMC7792329 DOI: 10.1186/s12870-020-02793-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 07/25/2020] [Accepted: 12/09/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pilea is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of Pilea, which limits our understanding of this genus. Here, we report 4 plastid genomes of Pilea taxa (Pilea mollis, Pilea glauca 'Greizy', Pilea peperomioides and Pilea serpyllacea 'Globosa') and performed comprehensive comparative analysis. RESULTS The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified (petN-psbM, psbZ-trnG-GCC, trnT-UGU-trnL-UAA, accD-psbI, ndhF-rpl32, rpl32-trnL-UAG, ndhA-intron and ycf1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of Pilea in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae. CONCLUSION Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of Pilea. The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.
Collapse
Affiliation(s)
- Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jianmin Tang
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Siyuan Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Fang Han
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jing Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, 400716, China.
| |
Collapse
|
43
|
Johnson BN, Quashie MLA, Chaix G, Camus‐Kulandaivelu L, Adjonou K, Segla KN, Kokutse AD, Ouinsavi C, Bationo BA, Rabiou H, Kokou K, Vignes H. Isolation and characterization of microsatellite markers for the threatened African endemic tree species Pterocarpus erinaceus Poir. Ecol Evol 2020; 10:13403-13411. [PMID: 33304547 PMCID: PMC7713909 DOI: 10.1002/ece3.6944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/30/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 11/10/2022] Open
Abstract
To study the genetic diversity and structure of the forest species Pterocarpus erinaceus Poir., seventeen polymorphic nuclear microsatellite markers were isolated and characterized, using next-generation sequencing. Three hundred and sixty-five (365) individuals were analyzed within fifteen (15) West African populations. The number of alleles for these loci varied from 4 to 30, and the heterozygosity varied from 0.23 to 0.82. The seventeen (17) primers designed here will allow characterizing the genetic diversity of this threaten species on its natural stands and to better understand the population differentiation mechanisms shaping it.
Collapse
Affiliation(s)
| | | | - Gilles Chaix
- CIRAD, UMR AGAPMontpellierFrance
- AGAPUniv MontpellierCIRAD, INRAeInstitut AgroMontpellierFrance
| | | | - Kossi Adjonou
- Laboratoire de Recherche Forestière (LRF)Université de LoméLoméTogo
| | | | | | - Christine Ouinsavi
- Laboratoire d'Etudes et de Recherches ForestièresFaculté d'AgronomieUniversité de ParakouParakouBénin
| | | | - Habou Rabiou
- Faculté des Sciences Agronomiques (FSA)Université de DiffaDiffaNiger
| | - Kouami Kokou
- Laboratoire de Recherche Forestière (LRF)Université de LoméLoméTogo
| | - Hélène Vignes
- CIRAD, UMR AGAPMontpellierFrance
- AGAPUniv MontpellierCIRAD, INRAeInstitut AgroMontpellierFrance
| |
Collapse
|