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Wang J, Kan J, Wang J, Yan X, Li Y, Soe T, Tembrock LR, Xing G, Li S, Wu Z, Jia M. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. FRONTIERS IN PLANT SCIENCE 2024; 15:1404071. [PMID: 38887455 PMCID: PMC11181306 DOI: 10.3389/fpls.2024.1404071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/29/2024] [Indexed: 06/20/2024]
Abstract
Backgrounds Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, 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, China
| | - Junhu Kan
- 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, 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, China
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xinlin Yan
- 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, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yi Li
- 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, China
| | - Thida Soe
- 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, China
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Zhiqiang Wu
- College of Horticulture, Shanxi Agricultural University, Jinzhong, 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, China
| | - Minlong Jia
- College of Horticulture, Shanxi Agricultural University, Jinzhong, 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, China
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Vintsek L, Klichowska E, Nowak A, Nobis M. Insight into the phylogeny and responses of species from the genus Sergia (Campanulaceae) to the climate changes predicted for the Mountains of Central Asia (a world biodiversity hotspot). BMC PLANT BIOLOGY 2024; 24:228. [PMID: 38561665 PMCID: PMC10986085 DOI: 10.1186/s12870-024-04938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Together with other elevated areas, the Mountains of Central Asia are significantly threatened by ongoing climate change. The presence of refuges during the glaciations makes the region extremely rich in species, especially endemic ones. However, the limited potential for colonisation of other habitats makes rocky-related species with 'island-like' distribution, particularly vulnerable to climate change. To understand the processes underlying species response to climate warming, we assessed differences in ecological niches and phylogenetic relationship of two geographically disjunctive alpine species belonging to the genus Sergia. The taxa are considered Tertiary relicts, endemic to the Tian Shan and Pamir-Alai Mountains. To illustrate range dynamics and differences in occupied niches of Sergia species, we used Ecological Niche Modelling of current and future distribution. Whereas, to reconstruct the phylogenetic relationship within and between Sergia and other related Campanulaceae species from the region we used molecular data (ITS, cpDNA, DArTseq-derived SNPs). RESULTS The results reveal that the genus Sergia is a polyphyletic group, and its representatives differ geographically, ecologically and genetically. Both S. regelii and S. sewerzowii constitute a common clade with Asyneuma group, however, S. sewerzowii is more closely related to Campanula alberti (a species that has never previously been considered closely related to the genus Asyneuma or Sergia) than to S. regelii. Sergia sewerzowii is adapted to lower elevations with higher temperatures, while S. regelii prefers higher elevations with lower temperatures. The future distribution models demonstrate a dramatic loss of S. regelii range with a shift to suitable habitats in higher elevations, while the potential range of S. sewerzowii increases and shifts to the north. CONCLUSIONS This study shows that S. regelii and S. sewerzowii have a long and independent evolution history. Sergia regelii and S. sewerzowii significantly differ in realised niches. These differences are mirrored in the response of the studied endemics to future climate warming. As suitable habitats shrink, rapid changes in distribution can lead to species' range loss, which is also directly related to declines in genetic variability. The outcomes of this paper will help to more precisely assess the impact of climate changes on rocky-related plant species found in this world's biodiversity hotspot.
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Affiliation(s)
- Lizaveta Vintsek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, Warsaw, 02-973, Poland
- Botanical Garden of the Wrocław University, Sienkiewicza 23, 50-335, Wrocław, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, Kraków, 30-387, Poland.
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Liu X, Zhang D, Yu Z, Zeng B. Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond ( Prunus tenella). Front Genet 2024; 14:1329060. [PMID: 38283144 PMCID: PMC10811783 DOI: 10.3389/fgene.2023.1329060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.
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Affiliation(s)
| | | | | | - Bin Zeng
- College of Horticulture, Xinjiang Agricultural University, Urumqi, China
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Su N, Hodel RG, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, Wen J. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. PLANT DIVERSITY 2023; 45:397-408. [PMID: 37601549 PMCID: PMC10435964 DOI: 10.1016/j.pld.2023.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 08/22/2023]
Abstract
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Richard G.J. Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Jun-Ru Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Si-Yu Xie
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Chao-Xia Gui
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, CA 95616, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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Abdulrahman SS, Daştan SD, Shahbaz SE, Selamoglu Z. Phylogenetic Analysis of Prunus Genus Using Nuclear and Chloroplast Gene Markers as a Bioorganic Structure Profiling. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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Chromosome-Level Assembly of Flowering Cherry ( Prunus campanulata) Provides Insight into Anthocyanin Accumulation. Genes (Basel) 2023; 14:genes14020389. [PMID: 36833316 PMCID: PMC9957189 DOI: 10.3390/genes14020389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.
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Phylogenomic analysis and development of molecular markers for the determination of twelve plum cultivars (Prunus, Rosaceae). BMC Genomics 2022; 23:745. [PMID: 36348277 PMCID: PMC9644608 DOI: 10.1186/s12864-022-08965-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Background Plums are one of the most important economic crops of the Rosaceae family and are produced all over the world. China has many local varieties, but the genomic information is limited for genetic studies. Here, we first sequenced, assembled, and analyzed the plastomes of twelve plum cultivars and developed molecular markers to distinguish them. Results The twelve plastomes of plum cultivars have a circular structure of 157,863–157,952 bp containing a large single-copy region (LSC) of 86,109–86,287 bp, a small copy region (SSC) of 18,927–19,031 bp, and two inverted repeats (IR) of 26,353–26,387 bp each. The plastomes of plum cultivars encode 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. We detected 50, 54, 54, 53, 53, 50, 54, 54, 54, 49, 50, 54 SSRs in the twelve analyzed varieties, respectively. For repeat sequences, we identified 553 tandem repeats, 204 direct repeats, and 270 palindromic repeats. We also analyzed the expansion/contraction of IR regions. The genes rpl22, rps19, rpl2, ycf1, ndhF, and the trnH span on or near the boundary of IR and single-copy regions. Phylogenetic analysis showed that the twelve cultivars were clustered with the P. salicina and P. domestica. We developed eight markers LZ01 to LZ08 based on whole plastomes and nuclear genes and validated them successfully with six repetitions. Conclusions The results obtained here could fill in the blanks of the plastomes of these twelve plum cultivars and provide a wider perspective based on the basis of the plastomes of Prunus to the molecular identification and phylogenetic construction accurately. The analysis from this study provides an important and valuable resource for studying the genetic basis for agronomic and adaptive differentiation of the Prunus species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08965-z.
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Prunus lusitanica L. Fruits as a Novel Source of Bioactive Compounds with Antioxidant Potential: Exploring the Unknown. Antioxidants (Basel) 2022; 11:antiox11091738. [PMID: 36139810 PMCID: PMC9495831 DOI: 10.3390/antiox11091738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Prunus lusitanica L., also known as Portuguese laurel or locally known as ‘azereiro’, is a rare species with ornamental and ecological value. Only two studies regarding the bioactivity and chemical composition of its leaves were reported to date. Thus, the present study aims to qualitatively and quantitatively evaluate the phenolic profile, through HPLC-PAD-ESI-MS/MS (high-performance liquid chromatography–photodiode array detection–electrospray ionization tandem mass spectrometry), as well as the radical scavenging capacity, through ABTS (2,2’-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) and DPPH (2,2-diphenyl-1 picrylhydrazyl), and the reducing power (FRAP, ferric reducing antioxidant power) assays, of P. lusitanica fruits during a 4-year study. In total, 28 compounds were identified and quantified in the fruits, including 21 hydroxycinnamic acids (60.3%); 2 flavan-3-ols (27.9%), 2 anthocyanins (10.5%), 2 flavonols (1.0%), and 1 secoiridoid (0.3%). High antioxidant capacity was observed, with ABTS values ranging from 7.88 to 10.69 mmol TE (Trolox equivalents)/100 g fw (fresh weight), DPPH values from 5.18 to 8.17 mmol TE/100 g fw, and FRAP values from 8.76 to 11.76 mmol TE/100 g fw. According to these results, it can be concluded that these are rich sources of phenolic compounds with very promising antioxidant capacity and, therefore, with potential applications in the food and/or phytopharmaceutical sectors.
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Li M, Song YF, Sylvester SP, Sylvester SP, Wang XR. Comparative analysis of the complete plastid genomes in Prunus subgenus Cerasus (Rosaceae): Molecular structures and phylogenetic relationships. PLoS One 2022; 17:e0266535. [PMID: 35385520 PMCID: PMC8985974 DOI: 10.1371/journal.pone.0266535] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
Prunus subgenus Cerasus (cherry) is an economically important group that distributed in temperate regions of the northern hemisphere. However, shared interspecific morphological traits and variability across taxa of Cerasus are among the impediments to taxonomic efforts to correctly delimit taxa. This is further complicated by a lack of genetic information on these taxa, with no focused genomic or phylogenetic studies being done on Cerasus. In this study, we conducted comparative analysis on the complete plastid genomes (plastomes) of 20 Cerasus species to gain a greater understanding of the attributes of the plastome of these taxa while helping resolve their phylogenetic placement in Prunus sensu lato and interspecific relationships within the subgenus. Our results displayed that (1) the plastomes of the 20 Cerasus species studied exhibited a typical quadripartite structure with conversed genome arrangement, structure, and moderate divergence. (2) The average size of complete plastomes for the Cerasus taxa studied was 157,861 bp, ranging from 157,458 to 158,024 bp. A total of 134 genes were annotated, including 86 protein-coding genes, 40 tRNAs, and 8 rRNAs across all species. In simple sequence repeat analysis, we found Cerasus had a comparable number of dispersed and tandem repeats to those identified in other angiosperm taxa, with only P. pseudocerasus found to contain trinucleotide repeats. Nucleotide diversity analysis revealed that the trnG-GCC gene and rpl32-trnL region had the highest Pi value showing potential as phylogenetic markers. (3) Two phylogenetic trees of the plastomes verified the monophyletic relationship of Cerasus and provided a more resolved species-level phylogeny. Our study provides detailed plastome information for exploring the phylogeny of subg. Cerasus taxa. We identified various types of repeats and nucleotide diversity hotspots, which can be a reference for species identification and reconstruction of phylogenetic relationships.
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Affiliation(s)
- Meng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yan-Feng Song
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Steven P. Sylvester
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Steven P. Sylvester
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xian-Rong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
- * E-mail:
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Niu J, Zhu Q, Zeng J. The complete chloroplast genome of Prunus tangutica (Batal.) Korsh. Mitochondrial DNA B Resour 2022; 7:224-225. [PMID: 35087935 PMCID: PMC8788344 DOI: 10.1080/23802359.2021.1997110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Jinfeng Niu
- Ningxia State-owned Forest Farm and Forest Seedling Station, Yinchuan, Ningxia, China
| | - Qiang Zhu
- Ningxia Forestry Institute Co., Ltd, Yinchuan, Ningxia, China
- State Key Laboratory of Seeding Bioengineering, Yinchuan, Ningxia, China
| | - Jijuan Zeng
- Ningxia Forestry Institute Co., Ltd, Yinchuan, Ningxia, China
- State Key Laboratory of Seeding Bioengineering, Yinchuan, Ningxia, China
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Zhao C, Zhang Y, Qin H, Wang C, Huang X, Yang L, Yu T, Xu X, Luo X, Qin Q, Liu S. Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus. BMC Ecol Evol 2021; 21:201. [PMID: 34740327 PMCID: PMC8569995 DOI: 10.1186/s12862-021-01918-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Background Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 100, RR) (abbreviated as RCC). Ribosome DNA (rDNA) is often used to study molecular evolution of repeated sequences because it has high copy number and special conserved coding regions in genomes. In this study, we analysed the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S ribosomal RNA (rRNA) genes in 4nRR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish. Results Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4nRR and RCC. This study also identified two different types of ITS2 region in 4nRR and predicted the secondary structure of ITS2. It turns out that both secondary structures are functional. Compared with RCC, there was no significant difference in NTS (5S rRNA) methylation level, but the expression level of 5S rRNA was lower in 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S rRNA) was hypermethylated in 4nRR compared to RCC, but the expression of 18S rRNA gene was no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR. Conclusion The above studies initially revealed the effects of autotetraploidization on the structure and function of 5S and 45S rRNA in Carassius auratus, and provided a theoretical support for the systematic study of the evolution pattern and characteristics of rDNA in vertebrates.
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Affiliation(s)
- Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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12
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Larcenaire C, Wang F, Holásková I, Turcotte R, Gutensohn M, Park YL. Characterization of the Insect Assemblage and Associated Floral Volatiles of Black Cherry (Prunus serotina). PLANTS 2021; 10:plants10102195. [PMID: 34686004 PMCID: PMC8538322 DOI: 10.3390/plants10102195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 01/14/2023]
Abstract
Black cherry is an ecologically important high-value wood. A decline of its regeneration has been reported in the USA, which could be associated with a lack of pollination. This study was conducted to identify insects visiting black cherry flowers, to determine whether insects captured on the flowers carry black cherry pollen and to identify the volatile organic compounds (VOCs) emitted by flowers of black cherry. A two-year insect survey was conducted before, during and after the black cherry bloom. A total of 9533 insects were captured in traps and Diptera was the most abundant (64.1%). Significantly more insects in Diptera, Lepidoptera and Thysanoptera were captured in the traps installed in the canopy than those on the ground, and Anthalia bulbosa (Diptera: Hybotidae) was the dominant species. Electron microscopy analyses demonstrated that insects captured in the canopy indeed carried black cherry pollen. Black cherry flowers emitted a VOC blend that is composed of 34 compounds and dominated by β-ocimene and several phenylpropanoids/benzenoids. This floral VOC profile is similar to that of other pollinator-dependent Prunus species. This study reports pollinator insects and associated VOCs, for the first time, that could play a significant role in the pollination and regeneration of black cherry.
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Affiliation(s)
- Craig Larcenaire
- Forest Health Protection, USDA Forest Service, Morgantown, WV 26505, USA; (C.L.); (R.T.)
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA; (F.W.); (M.G.)
| | - Fumin Wang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA; (F.W.); (M.G.)
| | - Ida Holásková
- Office of Statistics, West Virginia Agriculture and Forestry Experiment Station, West Virginia University, Morgantown, WV 26506, USA;
| | - Richard Turcotte
- Forest Health Protection, USDA Forest Service, Morgantown, WV 26505, USA; (C.L.); (R.T.)
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA; (F.W.); (M.G.)
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA; (F.W.); (M.G.)
| | - Yong-Lak Park
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA; (F.W.); (M.G.)
- Correspondence: ; Tel.: +1-304-293-2882
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13
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Su N, Liu BB, Wang JR, Tong RC, Ren C, Chang ZY, Zhao L, Potter D, Wen J. On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology. FRONTIERS IN PLANT SCIENCE 2021; 12:743643. [PMID: 34707629 PMCID: PMC8542774 DOI: 10.3389/fpls.2021.743643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 05/23/2023]
Abstract
The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Bin-bin Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
| | - Jun-ru Wang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Ru-chang Tong
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Zhao-yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- Herbarium of Northwest A&F University, Yangling, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, Davis, CA, United States
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, United States
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14
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Du Z, Lu K, Zhang K, He Y, Wang H, Chai G, Shi J, Duan Y. The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time. BMC Genomics 2021; 22:645. [PMID: 34493218 PMCID: PMC8425060 DOI: 10.1186/s12864-021-07968-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 11/21/2022] Open
Abstract
Background Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus. Results The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya. Conclusion Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07968-6.
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Affiliation(s)
- Zhongyu Du
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China.,School of Ecology and environment, Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
| | - Ke Lu
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Kai Zhang
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Yiming He
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Haitao Wang
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Guaiqiang Chai
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Jianguo Shi
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Yizhong Duan
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China.
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15
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Haq SAU, Mir MA, Lone SM, Banoo A, Shafi F, Mir SA, Bhat JIA, Rashid R, Wani SH, Masoodi TH, Khan MN, Nehvi FA, Masoodi KZ. Explicating genetic diversity based on ITS characterization and determination of antioxidant potential in sea buckthorn (Hippophae spp.). Mol Biol Rep 2021; 49:5229-5240. [PMID: 34387804 DOI: 10.1007/s11033-021-06619-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Sea buckthorn (Hippophae) is in the focus of interest mainly for its positive effects on health of both human and animal organisms. Due to the similarities in vegetative morphology, Hippophae species are often misidentified. Therefore, current study was focused on ITS based sequence characterization of sea buckthorn species and comparative biochemical evaluation for its antioxidant properties. METHODS AND RESULTS DNA was extracted from leaf samples. Primer pairs K-Lab-SeaBukRhm-ITS1F1- K-Lab-SeaBukRhm-ITS1R1 and K-LabSeaBukTib- ITSF1- K-LabSeaBukTib-ITSR1 were used for PCR amplification. The purified PCR products were outsourced for sequencing. Phylogenetic tree was constructed based on neighbor-joining (NJ) method. Moreover, comparison of antioxidant potential of leaves of two sea buckthorn species (Hippophae rhamnoides and Hippophae tibetana) collected from different regions of Ladakh viz., Stakna, Nubra, DRDO Leh and Zanskar was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azino-bis (3- ethylbenzothiazoline-6-sulphonic acid) diammonium salt (ABTS), and Total antioxidant capacity (TAC) by phosphomolybdenum assays. The present investigation led to the differentiation of two sea buckthorn species viz., H. rhamnoides and H. tibetana based on Internal Transcribed Spacer (ITS) region. Moreover, significant variation was observed in antioxidant potential of leaf extracts collected from different regions. CONCLUSIONS Primary ITS sequence analysis was found to be powerful tool for identification and genetic diversity studies in sea buckthorn. Leaves of sea buckthorn have pronounced antioxidant properties and can be used in food, neutraceuticals and pharmaceutical industries etc. The current study will pave the way to discover small bioactive molecules responsible for antioxidant and anticancer properties in sea buckthorn.
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Affiliation(s)
- Syed Anam Ul Haq
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Mudasir A Mir
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Sameena M Lone
- Division of Vegetable Science, SKUAST-K, Srinagar, J&K, 190025, India
| | - Aqleema Banoo
- Division of Plant Pathology, SKUAST-K, Srinagar, J&K, 190025, India
| | - Fauzia Shafi
- Division of Basic Sciences and Humanities, SKUAST-K, Srinagar, J&K, 190025, India
| | - Shakeel A Mir
- Division of Agricultural Statistics, SKUAST-K, Srinagar, J&K, 190025, India
| | - Javeed I A Bhat
- Division of Environmental Sciences, SKUAST-K, Srinagar, J&K, 190025, India
| | - Rizwan Rashid
- Division of Vegetable Science, SKUAST-K, Srinagar, J&K, 190025, India
| | - Shabir H Wani
- Mountain Research Center for Field Crops, Khudwani,, SKUAST-K, Anantnag, J&K, 192102, India
| | - T H Masoodi
- Faculty of Forestry, Benihama-SKUAST-K, Ganderbal, J&K, 191201, India
| | - M N Khan
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Firdous A Nehvi
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India
| | - Khalid Z Masoodi
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K, 190025, India.
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16
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G J Hodel R, Zimmer E, Wen J. A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy. Mol Phylogenet Evol 2021; 160:107118. [PMID: 33609711 DOI: 10.1016/j.ympev.2021.107118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/01/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
The genus Prunus, which contains 250-400 species, has ample genomic resources for the economically important taxa in the group including cherries, peaches, and almonds. However, the backbone of Prunus, specifically the position of the racemose group relative to the solitary and corymbose groups, remains phylogenetically uncertain. Surprisingly, phylogenomic analyses to resolve relationships in the genus are lacking. Here, we assemble transcriptomes from 17 Prunus species representing four subgenera, and use existing transcriptome assemblies, to resolve key relationships in the genus using a phylogenomic approach. From the transcriptomes, we constructed 21-taxon datasets of putatively single-copy nuclear genes with 591 and 379 genes, depending on taxon-occupancy filtering. Plastome sequences were obtained or assembled for all species present in the nuclear data set. The backbone of Prunus was resolved consistently in the nuclear and chloroplast phylogenies, but we found substantial cytonuclear discord within subgenera. Our nuclear phylogeny recovered a monophyletic racemose group, contrasting with previous studies finding paraphyly that suggests repeated allopolyploidy early in the evolutionary history of the genus. However, we detected multiple species with histories consistent with hybridization and allopolyploidy, including a deep hybridization event involving subgenus Amygdalus and the Armeniaca clade in subgenus Prunus. Analyses of gene tree conflict revealed substantial discord at several nodes, including the crown node of the racemose group. Alternative gene tree topologies that conflicted with the species tree were consistent with a paraphyletic racemose group, highlighting the complex reticulated evolutionary history of this group.
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Affiliation(s)
- Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
| | - Elizabeth Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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17
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Li YL, Reed J, Xu YQ, Qu DH, Sun ZS. Complete chloroplast genome of Prunus fasciculata (Rosaceae), a species native to western North America. Mitochondrial DNA B Resour 2021; 6:480-482. [PMID: 33628896 PMCID: PMC7889079 DOI: 10.1080/23802359.2021.1872439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Yue-Ling Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - James Reed
- California Botanic Garden, Claremont, CA, USA
| | - Yu-Qian Xu
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Da-Hao Qu
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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18
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Phytopharmacological Possibilities of Bird Cherry Prunus padus L. and Prunus serotina L. Species and Their Bioactive Phytochemicals. Nutrients 2020; 12:nu12071966. [PMID: 32630652 PMCID: PMC7399899 DOI: 10.3390/nu12071966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/23/2020] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
Wild cherry is a plant observed in the form of trees or shrubs. This species comprises about twenty kinds of plants and the most popular are two, Prunus padus L. and Prunus serotina L., whose properties and content of phytochemical compounds are subject to studies. Wild cherry contains many active compounds, including tocopherols, vitamins, polyphenols and terpenes, which can have beneficial effects on health. On the other hand, wild cherry contains cyanogenic glycosides. Nevertheless, current research results indicate pro-health properties associated with both P. serotina and P. padus. The aim of this study was to collect and present the current state of knowledge about wild cherry and to review available in vitro and in vivo studies concerning its antioxidant, anti-inflammatory, antibacterial and antidiabetic activity. Moreover, the current work presents and characterizes phytochemical content in the leaves, bark and fruits of P. padus and P. serotina and compiles data that indicate their health-promoting and functional properties and possibilities of using them to improve health. We find that the anatomical parts of P. padus and P. serotina can be a valuable raw material used in the food, pharmaceutical and cosmetic industries as a source of bioactive compounds with multi-directional action.
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19
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Wang Q, Sun M, Zhang Y, Song Z, Zhang S, Zhang Q, Xu J, Liu H. Extensive chromosomal rearrangements and rapid evolution of novel effector superfamilies contribute to host adaptation and speciation in the basal ascomycetous fungi. MOLECULAR PLANT PATHOLOGY 2020; 21:330-348. [PMID: 31916390 PMCID: PMC7036362 DOI: 10.1111/mpp.12899] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/06/2019] [Accepted: 11/28/2019] [Indexed: 05/11/2023]
Abstract
The basal ascomycetes in genus Taphrina have strict host specificity and coevolution with their host plants, making them appealing models for studying the genomic basis of ecological divergence and host adaption. We therefore performed genome sequencing and comparative genomics of different Taphrina species with distinct host ranges to reveal their evolution. We identified frequent chromosomal rearrangements and highly dynamic lineage-specific (LS) genomic regions in Taphrina genomes. The LS regions occur at the flanking regions of chromosomal breakpoints, and are greatly enriched for DNA repeats, non-core genes, and in planta up-regulated genes. Furthermore, we identified hundreds of candidate secreted effector proteins (CSEPs) that are commonly organized in gene clusters that form distinct AT-rich isochore-like regions. Nearly half of the CSEPs constitute two novel superfamilies with modular structures unique to Taphrina. These CSEPs are commonly up-regulated during infection, enriched in the LS regions, evolved faster, and underwent extensive gene gain and loss in different species. In addition to displaying signatures of positive selection, functional characterization of selected CSEP genes confirmed their roles in suppression of plant defence responses. Overall, our results showed that extensive chromosomal rearrangements and rapidly evolving CSEP superfamilies play important roles in speciation and host adaptation in the early-branching ascomycetous fungi.
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Affiliation(s)
- Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Zhenzhen Song
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Qiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Jin‐Rong Xu
- Department of Botany and Plant PathologyPurdue UniversityWest LafayetteINUSA
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant ProtectionNorthwest A&F UniversityYanglingChina
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20
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Meeboon J, Takamatsu S, Braun U. Morphophylogenetic analyses revealed that Podosphaera tridactyla constitutes a species complex. Mycologia 2020; 112:244-266. [PMID: 32091967 DOI: 10.1080/00275514.2019.1698924] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Podosphaera tridactyla (s. lat.) is a powdery mildew species occurring on a wide range of Prunus spp. almost worldwide. We have investigated the phylogeny of the Po. tridactyla complex, with special emphasis on potential aspects of cryptic speciation. The results suggested that Po. tridactyla represents a species complex consisting of at least 12 different species. Based on detailed morphological examinations and molecular sequence analyses, we propose dividing Po. tridactyla s. lat. into 10 species, encompassing 7 new species (Po. ampla, Po. pruni-avium, Po. pruni-cerasoidis, Po. prunigena, Po. pruni-lusitanicae, Po. prunina, and Po. pruni-japonicae) and 3 known species (Po. longiseta, Po. salatai, and Po. tridactyla s. str.). Oidium passerinii on Pr. laurocerasus is confirmed as a synonym of Po. tridactyla s. str. Epitypes are designated for Po. tridactyla and Oidium passerinii.
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Affiliation(s)
- Jamjan Meeboon
- Graduate School of Bioresources, Mie University, 1577 Kurima-Machiya, Tsu, Mie 514-8507, Japan.,Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsu, Mie 514-2392, Japan
| | - Susumu Takamatsu
- Graduate School of Bioresources, Mie University, 1577 Kurima-Machiya, Tsu, Mie 514-8507, Japan.,Centre of Crop Protection, University of Southern Queensland, Toowoomba, Queensland, 4350, Australia
| | - Uwe Braun
- Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany
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21
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Guajardo V, Solís S, Almada R, Saski C, Gasic K, Moreno MÁ. Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function. Sci Rep 2020; 10:1467. [PMID: 32001784 PMCID: PMC6992769 DOI: 10.1038/s41598-020-58271-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/15/2019] [Indexed: 01/09/2023] Open
Abstract
Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks identification and studies of diversity in Prunus species. Also, given the high number of SNPs identified in exonic regions, this strategy represents an important tool for finding candidate genes underlying traits of interest and potential functional markers for use in marker-assisted selection.
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Affiliation(s)
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - María Ángeles Moreno
- Department of Pomology, Estación Experimental de Aula Dei-CSIC, 50059, Zaragoza, Spain.
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Zhao X, Yan M, Ding Y, Huo Y, Yuan Z. Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium 'Summit'. PeerJ 2019; 7:e8210. [PMID: 31879574 PMCID: PMC6927351 DOI: 10.7717/peerj.8210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear. METHODS In this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium 'Summit' from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively. RESULTS The complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium 'Summit' was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and 'Summit' cherry. A total of 73 simple sequence repeats (SSRs) were identified in 'Summit' cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.
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Affiliation(s)
- Xueqing Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ming Yan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yu Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yan Huo
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhaohe Yuan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
- College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
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Chwil M, Kostryco M, Matraszek-Gawron R. Comparative studies on structure of the floral nectaries and the abundance of nectar production of Prunus laurocerasus L. PROTOPLASMA 2019; 256:1705-1726. [PMID: 31312908 PMCID: PMC6820602 DOI: 10.1007/s00709-019-01412-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/03/2019] [Indexed: 05/09/2023]
Abstract
There is very scanty information concerning the floral nectary structure and nectar secretion in Prunus laurocerasus L. Therefore, the aim of the study was to determine the micromorphology, anatomy and ultrastructure of nectaries; the abundance of nectar production; and the quantitative and qualitative composition of sugars contained in the nectar of two P. laurocerasus cultivars: 'Schipkaensis' and 'Zabeliana'. The nectary structure was studied using light, fluorescence, scanning and transmission electron microscopy techniques. The nectar sugars were analysed with HPLC. The 'Schipkaensis' had longer inflorescences with a larger number of flowers and a longer perianth than 'Zabeliana'. The micromorphological structure of the nectaries in 'Schipkaensis' exhibited denser (approx. 39%) and larger (approx. 50%) stomata and thicker (approx. 13%) cuticular striae forming wider bands (approx. 26%) than in 'Zabeliana'. The results provide new data on the micromorphology, anatomy and ultrastructure of these floral nectaries. Nectary cuticle ornamentation as well as the size, type and density of stomata and stomatal complex topography can have a diagnostic value in Prunus. The nectar sugar weight indicates a significant apicultural value of the cherry laurel, especially in the case of 'Schipkaensis'. Cherry laurel is an entomophilous species recommended for cultivation in nectariferous zones and insect pollinator refuges; however, climatic conditions eliminating the invasiveness of these plants should be considered.
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Affiliation(s)
- Mirosława Chwil
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| | - Mikołaj Kostryco
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| | - Renata Matraszek-Gawron
- Department of Botany and Plant Physiology, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
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Bao W, Ao D, Wuyun T, Li T, Wang L, Liu H. The complete chloroplast genome of Prunus mira koehne (Prunoideae, Rosaceae), a wild and indigenous peach on Tibet, China. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3731-3733. [PMID: 33366164 PMCID: PMC7707581 DOI: 10.1080/23802359.2019.1679048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Prunus mira Koehne belonging to family Rosaceae, is an indigenous species distributed in Tibet, China. De novo assembly with low coverage whole genome sequencing data facilitated to generate the complete chloroplast (cp) genome of P. mira in this study. The genome was a circular DNA molecule with 158,153 bp in length. It exhibited a typical quadripartite structure comprising a large single-copy region (LSC, 86,319 bp), a small single-copy region (SSC, 19,022 bp) and a pair of inverted repeat regions (IRs, 26,406 bp each). A total of 112 genes were predicted, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that P. mira was the most ancestral and basal lineage within the subgenus Amygdalus (Prunoideae subfamily), which is conform to the traditional classification.
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Affiliation(s)
- Wenquan Bao
- College of Forestry, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Dun Ao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Tana Wuyun
- Non-timber Research and Development Center of Chinese Academy of Forestry, Zhengzhou, Henan, China.,Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Tiezhu Li
- Non-timber Research and Development Center of Chinese Academy of Forestry, Zhengzhou, Henan, China.,Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Lin Wang
- Non-timber Research and Development Center of Chinese Academy of Forestry, Zhengzhou, Henan, China.,Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, China
| | - Huimin Liu
- Non-timber Research and Development Center of Chinese Academy of Forestry, Zhengzhou, Henan, China.,Non-Timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou, Henan, China
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25
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Bielsa B, Sanz MÁ, Rubio-Cabetas MJ. Uncovering early response to drought by proteomic, physiological and biochemical changes in the almond × peach rootstock 'Garnem'. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:994-1008. [PMID: 31526467 DOI: 10.1071/fp19050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/15/2019] [Indexed: 06/10/2023]
Abstract
Drought affects growth and metabolism in plants. To investigate the changes in root protein function involved in the early response to drought stress, a proteomic analysis in combination to a physiological and biochemical analysis was performed in plants of 'Garnem', an almond × peach hybrid rootstock, subjected to short-term drought stress. Abscisic acid (ABA) accumulation levels increased during the drought exposure, which induced stomatal closure, and thus, minimised water losses. These effects were reflected in stomatal conductance and leaf water potential levels. However, 'Garnem' was able to balance water content and maintain an osmotic adjustment in cell membranes, suggesting a dehydration avoidance strategy. The proteomic analysis revealed significant abundance changes in 29 and 24 spots after 2 and 24 h of drought stress respectively. Out of these, 15 proteins were identified by LC-ESI-MS/MS. The abundance changes of these proteins suggest the influence in drought-responsive mechanisms present in 'Garnem', allowing its adaptation to drought conditions. Overall, our study improves existing knowledge on the root proteomic changes in the early response to drought. This will lead to a better understanding of dehydration avoidance and tolerance strategies, and finally, help in new drought-tolerance breeding approaches.
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Affiliation(s)
- Beatriz Bielsa
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA) - IA2 (CITA-Universidad de Zaragoza), Av. Montañana 930, 50059, Zaragoza, Spain
| | - María Á Sanz
- Área de Laboratorios de Análisis y Asistencia Tecnológica, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain
| | - María J Rubio-Cabetas
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA) - IA2 (CITA-Universidad de Zaragoza), Av. Montañana 930, 50059, Zaragoza, Spain; and Corresponding author.
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Baraket G, Abdallah D, Ben Mustapha S, Ben Tamarzizt H, Salhi-Hannachi A. Combination of Simple Sequence Repeat, S-Locus Polymorphism and Phenotypic Data for Identification of Tunisian Plum Species (Prunus spp.). Biochem Genet 2019; 57:673-694. [PMID: 30980219 DOI: 10.1007/s10528-019-09922-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 04/05/2019] [Indexed: 11/28/2022]
Abstract
Plums (Prunus spp.) are among the first fruit tree species that attracted human interest. Artificial crosses between wild and domesticated species of plums are still paving the way for creation of new phenotypic variability. In Tunisia, despite a considerable varietal richness of plum as well as a high economic value, the plum sector is experiencing a significant regression. The main reason of this regression is the absence of a national program of plum conservation. Hence, this work was aimed to phenotypically and genetically characterize 23 Tunisian plum accessions to preserve this patrimony. Closely related Prunus species from the same subgenus may be differing at two characteristics: ploidy level and phenotypic traits. In this study, single sequence repeat (SSR) markers allowed distinguishing between eighteen diploid accessions and five polyploid accessions, but SSR data alone precluded unambiguous ploidy estimation due to homozygosity. In contrast, S-allele markers were useful to identify the ploidy level between polyploid species, but they did not distinguish species with the same ploidy level. Seven out of 12 phenotypic traits were shown to be discriminant traits for plum species identification. Molecular and phenotypic traits were significantly correlated and revealed a powerful tool to draw taxonomic and genotypic keys. The results obtained in this work are of great importance for local Tunisian plum germplasm management.
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Affiliation(s)
- Ghada Baraket
- Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of Tunis, University of Tunis El Manar, Campus University, El Manar, 2092, Tunis, Tunisia.
| | - Donia Abdallah
- Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of Tunis, University of Tunis El Manar, Campus University, El Manar, 2092, Tunis, Tunisia
| | - Sana Ben Mustapha
- Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of Tunis, University of Tunis El Manar, Campus University, El Manar, 2092, Tunis, Tunisia
| | - Hend Ben Tamarzizt
- Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of Tunis, University of Tunis El Manar, Campus University, El Manar, 2092, Tunis, Tunisia
| | - Amel Salhi-Hannachi
- Laboratory of Molecular Genetics, Immunology & Biotechnology LR99ES12, Faculty of Sciences of Tunis, University of Tunis El Manar, Campus University, El Manar, 2092, Tunis, Tunisia
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Halász J, Kodad O, Galiba GM, Skola I, Ercisli S, Ledbetter CA, Hegedűs A. Genetic variability is preserved among strongly differentiated and geographically diverse almond germplasm: an assessment by simple sequence repeat markers. TREE GENETICS & GENOMES 2019; 15:12. [PMID: 0 DOI: 10.1007/s11295-019-1319-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/02/2019] [Accepted: 01/08/2019] [Indexed: 05/28/2023]
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28
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Wu B, Liu C, Potter D, Cui D. Taxonomic reconsideration of Prunusveitchii (Rosaceae). PHYTOKEYS 2019; 115:59-71. [PMID: 30692866 PMCID: PMC6345735 DOI: 10.3897/phytokeys.115.29219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Prunusveitchii was published in 1912 and was treated as a synonym of P.serrulatavar.pubescens. The information about this taxon is relatively scarce. When consulting specimens of Prunus L., type materials of Prunusveitchii were found to belong to three taxa and P.veitchii, P.concinna, P.japonicavar.zhejiangensis, C.jingningensis and C.xueluoensis were found to be conspecific. The taxonomic status of P.veitchii is reconsidered in the present paper. Morphometric analyses were performed to evaluate the significance of differences between P.veitchii and P.serrulatavar.pubescens. The results show that the leaves of P.veitchii are significantly smaller and narrower than the leaves of P.serrulatavar.pubescens and the peduncle and pedicels are shorter. According to the results of morphometric analyses, P.veitchii should be treated as a separate species. To address these results, a lectotype of P.veitchii is designated here and P.concinna, Cerasusjingningensis and C.xueluoensis are here designated as synonyms of P.veitchii.
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Affiliation(s)
- Baohuan Wu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaSouth China Agricultural UniversityGuangzhouChina
| | - Chaoyu Liu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaSouth China Agricultural UniversityGuangzhouChina
| | - Daniel Potter
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA 95616, USAUniversity of CaliforniaDavisUnited States of America
| | - Dafang Cui
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaSouth China Agricultural UniversityGuangzhouChina
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29
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Sokoloff DD, Ignatov MS, Remizowa MV, Nuraliev MS, Blagoderov V, Garbout A, Perkovsky EE. Staminate flower of Prunus s. l. (Rosaceae) from Eocene Rovno amber (Ukraine). JOURNAL OF PLANT RESEARCH 2018; 131:925-943. [PMID: 30032395 DOI: 10.1007/s10265-018-1057-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The late Eocene ambers provide plethora of animal and plant fossils including well-preserved angiosperm flowers from the Baltic amber. The Rovno amber from NW Ukraine resembles in many aspects the Baltic amber; however, only fossilized animals and some bryophytes have yet been studied from the Rovno amber. We provide the first detailed description of an angiosperm flower from Rovno amber. The flower is staminate with conspicuous hypanthium, double pentamerous perianth and whorled androecium of 24 stamens much longer than the petals. Sepals are sparsely pubescent and petals are densely hirsute outside. The fossil shares important features with extant members of Prunus subgen. Padus s. l. (incl. Laurocerasus, Pygeum and Maddenia), especially with its evergreen paleotropical species. It is described here as a new species Prunus hirsutipetala D.D.Sokoloff, Remizowa et Nuraliev. Our study provides the first convincing record of fossil flowers of Rosaceae from Eocene of Europe and the earliest fossil flower of Prunus outside North America. Our record of a plant resembling extant tropical species supports palaeoentomological evidences for warm winters in northwestern Ukraine during the late Eocene, as well as suggesting a more significant role of tropical insects in Rovno amber than inferred from Baltic amber.
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Affiliation(s)
- Dmitry D Sokoloff
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia.
| | - Michael S Ignatov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
- Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Botanicheskaya 4, 127276, Moscow, Russia
| | - Margarita V Remizowa
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
| | - Maxim S Nuraliev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | | | - Amin Garbout
- Core Research Labs, Natural History Museum, Cromwell Road, London, UK
| | - Evgeny E Perkovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, vul.B. Khmelnitskogo, 15, Kiev, 01030, Ukraine
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Stepanov IV, Trifonova AA, Kudryavtsev AM, Suprun II. Development of S-SAP Markers and Assessment of Their Potential in Genetic Studies of Representatives of the Genus Prunus L. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bielsa B, Hewitt S, Reyes-Chin-Wo S, Dhingra A, Rubio-Cabetas MJ. Identification of water use efficiency related genes in 'Garnem' almond-peach rootstock using time-course transcriptome analysis. PLoS One 2018; 13:e0205493. [PMID: 30308016 PMCID: PMC6181374 DOI: 10.1371/journal.pone.0205493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/19/2022] Open
Abstract
Drought is one of the main abiotic stresses with far-reaching ecological and socioeconomic impacts, especially in perennial food crops such as Prunus. There is an urgent need to identify drought resilient rootstocks that can adapt to changes in water availability. In this study, we tested the hypothesis that PEG-induced water limitation stress will simulate drought conditions and drought-related genes, including transcription factors (TFs), will be differentially expressed in response to this stress. 'Garnem' genotype, an almond × peach hybrid [P. amygdalus Batsch, syn P. dulcis (Mill.) x P. persica (L.) Batsch] was exposed to PEG-6000 solution, and a time-course transcriptome analysis of drought-stressed roots was performed at 0, 2 and 24 h time points post-stress. Transcriptome analysis resulted in the identification of 12,693 unique differentially expressed contigs (DECs) at the 2 h time point, and 7,705 unique DECs at the 24 h time point after initiation of the drought treatment. Interestingly, three drought-induced genes, directly related to water use efficiency (WUE) namely, ERF023 TF; LRR receptor-like serine/threonine-kinase ERECTA; and NF-YB3 TF, were found induced under stress. The RNAseq results were validated with quantitative RT-PCR analysis of eighteen randomly selected differentially expressed contigs (DECs). Pathway analysis in the present study provides valuable information regarding metabolic events that occur during stress-induced signalling in 'Garnem' roots. This information is expected to be useful in understanding the potential mechanisms underlying drought stress responses and drought adaptation strategies in Prunus species.
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Affiliation(s)
- Beatriz Bielsa
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
| | - Seanna Hewitt
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | | | - Amit Dhingra
- Molecular Plant Sciences, Washington State University, Pullman, Washington, United States of America
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America
| | - María José Rubio-Cabetas
- Hortofruticulture Department. Agrifood Research and Technology Centre of Aragon (CITA), Zaragoza, Spain
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Ruiz C, Nadal A, Foix L, Montesinos L, Montesinos E, Pla M. Diversity of plant defense elicitor peptides within the Rosaceae. BMC Genet 2018; 19:11. [PMID: 29361905 PMCID: PMC5782389 DOI: 10.1186/s12863-017-0593-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by bacteria, fungi and herbivores. Pep topic application and transgenic expression have been found to enhance disease resistance in a small number of model plant-pathogen systems. The action of Peps relies on perception by specific receptors, so displaying a family-specific activity. Recently, the presence and activity of Peps within the Rosaceae has been demonstrated. Here we characterized the population of Pep sequences within the economically important plant family of Rosaceae, with special emphasis on the Amygdaleae and Pyreae tribes, which include the most relevant edible species such as apple, pear and peach, and numerous ornamental and wild species (e.g. photinia, firethorn and hawthorn). RESULTS The systematic experimental search for Pep and the corresponding precursor PROPEP sequences within 36 Amygdaleae and Pyreae species, and 100 cultivars had a highly homogeneous pattern, with two tribe-specific Pep types per plant, i.e. Pep1 and Pep2 (Amygdaleae) or Pep3 and Pep4 (Pyreae). Pep2 and Pep3 are highly conserved, reaching identity percentages similar to those of genes used in plant phylogenetic analyses, while Pep1 and Pep4 are somewhat more variable, with similar values to the corresponding PROPEPs. In contrast to Pep3 and Pep4, Pep1 and Pep2 sequences of different species paralleled their phylogenetic relationships, and putative ancestor sequences were identified. The large amount of sequences allowed refining of a C-terminal consensus sequence that would support the protective activity of Pep1-4 in a Prunus spp. and Xanthomonas arboricola pv. pruni system. Moreover, tribe-specific consensus sequences were deduced at the center and C-terminal regions of Peps, which might explain the higher protection efficiencies described upon topic treatments with Peps from the same tribe. CONCLUSIONS The present study substantially enhances the knowledge on Peps within the Amygdaleae and Pyreae species. It can be the basis to design and fine-tune new control tools against important plant pathogens affecting Prunus, Pyrus and Malus species.
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Affiliation(s)
- Cristina Ruiz
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Anna Nadal
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Laura Foix
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Laura Montesinos
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Emilio Montesinos
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain
| | - Maria Pla
- Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain.
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Molaei H, Jahanbin K. Structural features of a new water-soluble polysaccharide from the gum exudates of Amygdalus scoparia Spach (Zedo gum). Carbohydr Polym 2017; 182:98-105. [PMID: 29279132 DOI: 10.1016/j.carbpol.2017.10.099] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/08/2017] [Accepted: 10/31/2017] [Indexed: 11/24/2022]
Abstract
A new water-soluble polysaccharide (CZGS-1) with molecular weight of 4860kDa and a specific optical rotation of +31.5° (c 1.0, H2O), was extracted from the gum exudate of Amygdalus scoparia Spach by hot water, following by purification with DEAE-cellulose A52 and Sephacryl S-400 HR columns. Monosaccharide composition analysis indicates that CZGS-1 was an arabino galactan including Rha, Ara, Xyl, and Gal with a relative molar ratio of 1.1:20:5.2:17.9. The uronic acid content of CZGS-1 was about 6%. Structural features of CZGS-1 was investigated by a combination of partial acid hydrolysis, methylation and GC-MS analysis, periodic acid oxidation and Smith degradation, FT-IR and NMR spectroscopy. The results indicated that CZGS-1 possesses a backbone of →3,6)-β-d-Galp-(1→, →3)-β-d-Galp-(1→, and →3)-α-l-Araf-(1→ residues with side chains attached to O-3 and O-6 positions of 1,3,6-linked β-d-Galp. The side chains are consisted of β-d-Xylp-(1→3)-α-l-Araf-(1→3)-α-l-Araf-(1→), α-l-Rhap-(1→6)-β-d-Galp-(1→), and β-d-GlcAp-(1→6)-β-d-Galp-(1→).
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Affiliation(s)
- Hamideh Molaei
- Shahrood University of Technology, School of Agricultural Engineering, Department of Food Science and Technology, Shahrood, Iran.
| | - Kambiz Jahanbin
- Shahrood University of Technology, School of Agricultural Engineering, Department of Food Science and Technology, Shahrood, Iran.
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Zimmers J, Thomas M, Yang L, Bombarely A, Mancuso M, Wojciechowski M, Smith J. Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques. Mol Phylogenet Evol 2017; 114:93-110. [DOI: 10.1016/j.ympev.2017.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/01/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
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Xiang Y, Huang CH, Hu Y, Wen J, Li S, Yi T, Chen H, Xiang J, Ma H. Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication. Mol Biol Evol 2017; 34:262-281. [PMID: 27856652 PMCID: PMC5400374 DOI: 10.1093/molbev/msw242] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.
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Affiliation(s)
- Yezi Xiang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA
| | - Jun Wen
- The Smithsonian Institution, Washington, DC
| | - Shisheng Li
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Tingshuang Yi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hongyi Chen
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Jun Xiang
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, School of Life Sciences, Huanggang Normal College, Huanggang, Hubei, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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Taxa of Rosaceae of the Ukrainian flora: position in a new system of the family according to molecular phylogenetic data. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Shabani H, Askari G, Jahanbin K, Khodaeian F. Evaluation of physicochemical characteristics and antioxidant property of Prunus avium gum exudates. Int J Biol Macromol 2016; 93:436-441. [DOI: 10.1016/j.ijbiomac.2016.08.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/12/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
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RETRACTED ARTICLE: Molecular Characterization of Prunus angustifolia Genotypes from Turkey. Biochem Genet 2016; 55:278-279. [PMID: 27562487 DOI: 10.1007/s10528-016-9767-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
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Zhao L, Jiang XW, Zuo YJ, Liu XL, Chin SW, Haberle R, Potter D, Chang ZY, Wen J. Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data. PLoS One 2016; 11:e0157123. [PMID: 27294529 PMCID: PMC4905661 DOI: 10.1371/journal.pone.0157123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 05/25/2016] [Indexed: 01/01/2023] Open
Abstract
Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.
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Affiliation(s)
- Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi-Wang Jiang
- College of Life Sciences, Jianghan University, Wuhan, Hubei, 430056, China
| | - Yun-juan Zuo
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences / Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai, 201602, China
| | - Xiao-Lin Liu
- School of Applied Chemistry and Biological Engineering, Weifang Engineering Vocational College, Qingzhou, Shandong, 262500, China
| | - Siew-Wai Chin
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Rosemarie Haberle
- Department of Biology, Pacific Lutheran University, Tacoma, Washington, 98447, United States of America
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
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Cho MS, Hyun Cho C, Yeon Kim S, Su Yoon H, Kim SC. Complete chloroplast genome of Prunus yedoensis Matsum.(Rosaceae), wild and endemic flowering cherry on Jeju Island, Korea. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3652-4. [PMID: 26329800 DOI: 10.3109/19401736.2015.1079840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome sequences of the wild flowering cherry, Prunus yedoensis Matsum., which is native and endemic to Jeju Island, Korea, is reported in this study. The genome size is 157 786 bp in length with 36.7% GC content, which is composed of LSC region of 85 908 bp, SSC region of 19 120 bp and two IR copies of 26 379 bp each. The cp genome contains 131 genes, including 86 coding genes, 8 rRNA genes and 37 tRNA genes. The maximum likelihood analysis was conducted to verify a phylogenetic position of the newly sequenced cp genome of P. yedoensis using 11 representatives of complete cp genome sequences within the family Rosaceae. The genus Prunus exhibited monophyly and the result of the phylogenetic relationship agreed with the previous phylogenetic analyses within Rosaceae.
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Affiliation(s)
- Myong-Suk Cho
- a Department of Biological Sciences , Sungkyunkwan University , Suwon , Republic of Korea
| | - Chung Hyun Cho
- a Department of Biological Sciences , Sungkyunkwan University , Suwon , Republic of Korea
| | - Su Yeon Kim
- a Department of Biological Sciences , Sungkyunkwan University , Suwon , Republic of Korea
| | - Hwan Su Yoon
- a Department of Biological Sciences , Sungkyunkwan University , Suwon , Republic of Korea
| | - Seung-Chul Kim
- a Department of Biological Sciences , Sungkyunkwan University , Suwon , Republic of Korea
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Cho MS, Kim CS, Kim SH, Kim TO, Heo KI, Jun J, Kim SC. Molecular and morphological data reveal hybrid origin of wild Prunus yedoensis (Rosaceae) from Jeju Island, Korea: implications for the origin of the flowering cherry. AMERICAN JOURNAL OF BOTANY 2014; 101:1976-86. [PMID: 25366862 DOI: 10.3732/ajb.1400318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY The subgenus Cerasus of the genus Prunus includes several popular ornamental flowering cherries. Of the hundreds of cultivars, P. ×yedoensis ('Somei-yoshino') is the most popular and familiar cultivar in Korea and Japan and is considered to be of hybrid origin. However, the hybrid origin of P. ×yedoensis and its relationship to wild P. yedoensis, naturally occurring on Jeju Island, Korea, are highly controversial. METHODS We extensively sampled wild P. yedoensis, cultivated P. ×yedoensis, and numerous individuals from other species belonging to subgenus Cerasus on Jeju Island. Samples from 71 accessions, representing 13 species and one cultivar (P. ×yedoensis), were sequenced for nrDNA ITS/ETS (952 characters) and seven noncoding cpDNA regions (5421 characters) and subjected to maximum parsimony and maximum likelihood analysis. Additive polymorphisms in the ITS/ETS regions were confirmed by cloning amplicons from representative species. KEY RESULTS The nuclear (ITS/ETS and G3pdh) and cpDNA data, along with several morphological characteristics, provide the first convincing evidence for the hybrid origin of wild P. yedoensis. The maternal parent was determined to be P. spachiana f. ascendens, while the paternal parent was unresolved from the taxonomically complex P. serrulata/P. sargentii clade. The presence of two kinds of ribotypes was confirmed by cloning, and the possible origin of cultivated P. ×yedoensis from wild populations on Jeju Island was also suggested. CONCLUSIONS Bidirectional and multiple hybridization events were responsible for the origin of wild P. yedoensis. Extensive gene flow was documented in this study, suggesting an important role of reticulate evolution in subgenus Cerasus.
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Affiliation(s)
- Myong-Suk Cho
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 440-746, Korea
| | - Chan-Soo Kim
- Warm-Temperate and Subtropical Forest Research Center, Korea Forest Research Institute, Seogwipo, Jeju 967-050, Korea
| | - Seon-Hee Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 440-746, Korea
| | - Ted Oh Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 440-746, Korea
| | - Kyoung-In Heo
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 440-746, Korea
| | - Jumin Jun
- National Institute of Biological Resources, Nanji-ro 42, Seo-gu, Incheon, 404-708, Korea
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 440-746, Korea
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Physicochemical characteristics and antioxidant activity of Prunus cerasoides D. Don gum exudates. Int J Biol Macromol 2014; 69:192-9. [DOI: 10.1016/j.ijbiomac.2014.05.050] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/20/2022]
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Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae). Mol Phylogenet Evol 2014; 76:34-48. [DOI: 10.1016/j.ympev.2014.02.024] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/15/2013] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
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Shi S, Li J, Sun J, Yu J, Zhou S. Phylogeny and classification of Prunus sensu lato (Rosaceae). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:1069-79. [PMID: 23945216 DOI: 10.1111/jipb.12095] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 07/22/2013] [Indexed: 05/26/2023]
Abstract
The classification of the economically important genus Prunus L. sensu lato (s.l.) is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.l. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions (atpB-rbcL, matK, ndhF, psbA-trnH, rbcL, rpL16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycf1) and three nuclear genes (ITS, s6pdh and SbeI) to explore their infrageneric relationships. The results of these analyses were used to develop a new, phylogeny-based classification of Prunus s.l. Our phylogenetic reconstructions resolved three main clades of Prunus s.l. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades: subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae (T. T. Yü & L. T. Lu) S. L. Zhou and one new species name, Prunus tianshanica (Pojarkov) S. Shi, were proposed.
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Affiliation(s)
- Shuo Shi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100043, China
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Sun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M. Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.). BMC Genet 2013; 14:98. [PMID: 24093913 PMCID: PMC3851432 DOI: 10.1186/1471-2156-14-98] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 09/25/2013] [Indexed: 11/10/2022] Open
Abstract
Background Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume ‘Fenban’ and Prunus mume ‘Kouzi Yudie’ to identify high-quality polymorphic markers between the two cultivars on a large scale. Results A total of 1464.1 Mb and 1422.1 Mb of ‘Fenban’ and ‘Kouzi Yudie’ sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent’s SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny. Conclusions A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between ‘Fenban’ and ‘Kouzi Yudie’ using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, 100083 Beijing, P,R, China.
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Liu XL, Wen J, Nie ZL, Johnson G, Liang ZS, Chang ZY. Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America. JOURNAL OF PLANT RESEARCH 2013; 126:351-361. [PMID: 23239308 DOI: 10.1007/s10265-012-0535-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 10/17/2012] [Indexed: 06/01/2023]
Abstract
Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59-6.15)-4.1 (95 % HPD 0.63-8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.
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Affiliation(s)
- Xiao-Lin Liu
- College of Life Science, Northwest Agriculture and Forest University, Yangling, Shaanxi, China.
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Wang H, Walla JA, Zhong S, Huang D, Dai W. Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.). PLANT CELL REPORTS 2012; 31:2047-2055. [PMID: 22837059 DOI: 10.1007/s00299-012-1315-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/25/2012] [Accepted: 07/11/2012] [Indexed: 06/01/2023]
Abstract
Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8 Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100 bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2 %) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7 % of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2 % of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species. Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.
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Affiliation(s)
- Hongxia Wang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
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Microsatellite variations and population structure in an on-farm collection of Japanese apricot (Prunus mume Sieb. et Zucc.). BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Anwar F, Manzoor M, Ashraf M, Alkharfy KM. Physico-chemical characteristics of seed oils extracted from different apricot ( Prunus armeniaca L.) varieties from Pakistan. GRASAS Y ACEITES 2012. [DOI: 10.3989/gya.095011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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