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Huang L, Xu Y, Valcárcel V, Lutz S, Wen J, Ren Z. Three complete chloroplast genomes from two north American Rhus species and phylogenomics of Anacardiaceae. BMC Genom Data 2024; 25:30. [PMID: 38491489 PMCID: PMC10943888 DOI: 10.1186/s12863-024-01200-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/30/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The suamc genus Rhus (sensu stricto) includes two subgenera, Lobadium (ca. 25 spp.) and Rhus (ca. 10 spp.). Their members, R. glabra and R. typhina (Rosanae: Sapindales: Anacardiaceae), are two economic important species. Chloroplast genome information is of great significance for the study of plant phylogeny and taxonomy. RESULTS The three complete chloroplast genomes from two Rhus glabra and one R. typhina accessions were obtained with a total of each about 159k bp in length including a large single-copy region (LSC, about 88k bp), a small single-copy regions (SSC, about 19k bp) and a pair of inverted repeats regions (IRa/IRb, about 26k bp), to form a canonical quadripartite structure. Each genome contained 88 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes and two pseudogenes. The overall GC content of the three genomes all were same (37.8%), and RSCU values showed that they all had the same codon prefers, i.e., to use codon ended with A/U (93%) except termination codon. Three variable hotspots, i.e., ycf4-cemA, ndhF-rpl32-trnL and ccsA-ndhD, and a total of 152-156 simple sequence repeats (SSR) were identified. The nonsynonymous (Ka)/synonymous (Ks) ratio was calculated, and cemA and ycf2 genes are important indicators of gene evolution. The phylogenetic analyses of the family Anacardiaceae showed that the eight genera were grouped into three clusters, and supported the monophyly of the subfamilies and all the genera. The accessions of five Rhus species formed four clusters, while, one individual of R. typhina grouped with the R. glabra accessions instead of clustering into the two other individuals of R. typhina in the subgenus Rhus, which showed a paraphyletic relationship. CONCLUSIONS Comparing the complete chloroplast genomes of the Rhus species, it was found that most SSRs were A/T rich and located in the intergenic spacer, and the nucleotide divergence exhibited higher levels in the non-coding region than in the coding region. The Ka/Ks ratio of cemA gene was > 1 for species collected in America, while it was < 1 for other species in China, which dedicated that the Rhus species from North America and East Asia have different evolutionary pressure. The phylogenetic analysis of the complete chloroplast genome clarified the Rhus placement and relationship. The results obtained in this study are expected to provide valuable genetic resources to perform species identification, molecular breeding, and intraspecific diversity of the Rhus species.
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Affiliation(s)
- Lan Huang
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Yujie Xu
- School of Geosciences, Qinghai Normal University, 810008, Xining, Qinghai, China
| | - Virginia Valcárcel
- Departamento de Biología, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Centro de Investigación en Biodiversidady Cambio Global (CIBC-UAM) , Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Sue Lutz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, 20013, Washington, DC, USA.
| | - Zhumei Ren
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China.
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Chen Z, Liu Q, Xiao Y, Zhou G, Yu P, Bai J, Huang H, Gong Y. Complete chloroplast genome sequence of Camellia sinensis: genome structure, adaptive evolution, and phylogenetic relationships. J Appl Genet 2023; 64:419-429. [PMID: 37380816 DOI: 10.1007/s13353-023-00767-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
The chloroplast (cp) genome holds immense potential for a variety of applications including species identification, phylogenetic analysis, and evolutionary studies. In this study, we utilized Illumina NovaSeq 6000 to sequence the DNA of Camellia sinensis L. cultivar 'Zhuyeqi', followed by the assembly of its chloroplast genome using SPAdes v3.10.1, with subsequent analysis of its features and phylogenetic placement. The results showed that the cp genome of 'Zhuyeqi' was 157,072 bp, with a large single-copy region (LSC, 86,628 bp), a small single-copy region (SSC,18,282 bp), and two inverted repeat regions (IR, 26,081 bp). The total AT and GC contents of the cp genome of 'Zhuyeqi' were observed to be 62.21% and 37.29%, respectively. The cp genome encoded 135 unique genes, including 90 protein-coding genes (CDS), 37 tRNA genes, and 8 rRNA genes. Moreover, 31 codons and 247 simple sequence repeats (SSRs) were identified. The cp genomes of 'Zhuyeqi' were found to be relatively conserved, with conservation observed in the IR region, which showed no evidence of inversions or rearrangements. The five regions with the largest variations were identified, with four regions (rps12, rps19, rps16, and rpl33) located in the LSC region and one divergent region (trnI-GAU) in the IR region. Phylogenetic analysis revealed that Camellia sinensis (KJ996106.1) was closely related to 'Zhuyeqi', indicating a close phylogenetic relationship between these two species. These findings could provide important genetic information for further research into breeding of tea tree, phylogeny, and evolution of Camellia sinensis.
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Affiliation(s)
- Zhiyin Chen
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Qing Liu
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Ying Xiao
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Guihua Zhou
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Penghui Yu
- Tea Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jing Bai
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China
| | - Hua Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, 510640, People's Republic of China.
| | - Yihui Gong
- College of Agriculture & Biotechnology, Hunan University of Humanities, Science & Technology, Loudi, 417000, China.
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Oh DR, Choi C, Kim MJ, Mun BY, Ko H, Oh KN, Jo A, Kim JY, Bae D. Antidepressant effects of p-coumaric acid isolated from Vaccinium bracteatum leaves extract on chronic restraint stress mouse model and antagonism of serotonin 6 receptor in vitro. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154871. [PMID: 37270968 DOI: 10.1016/j.phymed.2023.154871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Vaccinium bracteatum Thunb. leaves (VBL) are used in traditional herbal medicines to treat various biological diseases. p-coumaric acid (CA), the main active component of VBL, has neuroprotective effects against corticosterone-induced damage in vitro. However, the effects of CA on immobility induced by chronic restraint stress (CRS) in a mouse model and 5-HT receptor activity have not been investigated. HYPOTHESIS/PURPOSE We investigated the antagonistic effects of VBL, NET-D1602, and the three components of Gαs protein-coupled 5-HT receptors. Additionally, we identified the effects and mechanism of action of CA, the active component of NET-D1602, in the CRS-exposed model. METHODS For in vitro analyses, we used 1321N1 cells stably expressing human 5-HT6 receptors and CHO-K1 expressing human 5-HT4 or 5-HT7 receptors cell lines to study the mechanism of action. For in vivo analyses, CRS-exposed mice were orally administered CA (10, 50, or 100 mg/kg) daily for 21 consecutive days. The effects of CA were analyzed by assessing behavioral changes using a forced swim test (FST), measuring levels of hypothalamic-pituitary-adrenal (HPA) axis-related hormones in ntial therapeutic effects as 5-HT6 receptor antagonists for neurodegenerative diseases and depressioserum, and acetylcholinesterase (AChE), monoamines, including 5-HT, dopamine, and norepinephrine, using enzyme-linked immunosorbent assay kits. The underlying molecular mechanisms of the serotonin transporter (SERT), monoamine oxidase A (MAO-A), and extracellular signal-regulated kinase (ERK)/protein kinase B (Akt)/mTORC1 signaling were detected using western blotting. RESULTS CA was confirmed to be an active component in the antagonistic effects of NET-D1602 on 5-HT6 receptor activity through decreases in cAMP and ERK1/2 phosphorylation. Moreover, CRS-exposed mice treated with CA showed a significantly reduced immobility time in the FST. CA also significantly decreased corticosterone, corticotropin-releasing hormone (CRH), and adrenocorticotropic hormone (ACTH) levels. CA enhanced 5-HT, dopamine, and norepinephrine levels in the hippocampus (HC) and prefrontal cortex (PFC) but decreased MAO-A and SERT protein levels. Similarly, CA significantly upregulated the ERK, Ca2+/calmodulin-dependent protein kinase II (CaMKII), Akt/mTOR/p70S6K/S6 signaling pathways in both HC and the PFC. CONCLUSION CA contained in NET-D1602 may play the antidepressant effects against CRS-induced depression-like mechanism and the selective antagonist effect of 5-HT6 receptor.
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Affiliation(s)
- Dool-Ri Oh
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea
| | - Chulyung Choi
- Department of Biomedical Science, College of Natural Science, Chosun University, 309, pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea; Department of Integrative Biological Sciences & BK21 FOUR Educational Research Group for Age-associated Disorder Control Technology, Chosun University, 309, pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Moon Jong Kim
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea
| | - Bo Yeong Mun
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea
| | - Haeju Ko
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea
| | - Kyo-Nyeo Oh
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea
| | - Ara Jo
- Department of Biomedical Science, College of Natural Science, Chosun University, 309, pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Jin Young Kim
- Department of Biomedical Science, College of Natural Science, Chosun University, 309, pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Donghyuck Bae
- Jeonnam Bioindustry Foundation, Jeonnam Institute of Natural Resources Research (JINR), 288, Woodland-gil, Anyang-myeon, Jangheung-gun, Jeollanamdo 59338, Republic of Korea.
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Koo H, Shin AY, Hong S, Kim YM. The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1111968. [PMID: 36818825 PMCID: PMC9931742 DOI: 10.3389/fpls.2023.1111968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Hibiscus syriacus, a member of the tribe Hibisceae, is considered an important ornamental and medicinal plant in east Asian countries. Here, we sequenced and assembled the complete chloroplast genome of H. syriacus var. Baekdansim using the PacBio long-read sequencing platform. A quadripartite structure with 161,026 base pairs was obtained, consisting of a pair of inverted repeats (IRA and IRB) with 25,745 base pairs, separated by a large single-copy region of 89,705 base pairs and a short single-copy region of 19,831 base pairs. This chloroplast genome had 79 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 109 simple sequence repeat regions. Among them, ndhD and rpoC1, containing traces of RNA-editing events associated with adaptive evolution, were identified by analysis of putative RNA-editing sites. Codon usage analysis revealed a preference for A/U-terminated codons. Furthermore, the codon usage pattern had a clustering tendency similar to that of the phylogenetic analysis of the tribe Hibisceae. This study provides clues for understanding the relationships and refining the taxonomy of the tribe Hibisceae.
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Affiliation(s)
- Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seongmin Hong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships. Genes (Basel) 2022; 13:genes13091550. [PMID: 36140718 PMCID: PMC9498446 DOI: 10.3390/genes13091550] [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: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.
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Darshetkar AM, Patil SS, Pable AA, Nadaf AB, Barvkar VT. Chloroplast genome sequence of Pandanus odorifer (Forssk.) Kuntze: genome features, mutational hotspots and phylogenetic analyses. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01155-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Karppinen K, Avetisyan A, Hykkerud AL, Jaakola L. A dPCR Method for Quantitative Authentication of Wild Lingonberry ( Vaccinium vitis-idaea) versus Cultivated American Cranberry ( V. macrocarpon). Foods 2022; 11:1476. [PMID: 35627046 PMCID: PMC9141823 DOI: 10.3390/foods11101476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023] Open
Abstract
Berries of the genus Vaccinium are highly valued health-beneficial superfoods, which are commonly subjected to adulteration and mixed with each other, or with other common berry species. A quantitative DNA-based method utilizing a chip-based digital polymerase chain reaction (dPCR) technique was developed for identifying and quantifying wild lingonberry (V. vitis-idaea) and cultivated American cranberry (V. macrocarpon). The dPCR method with species-specific primers for mini-barcoding was designed based on the indel regions found in the trnI-CAU-trnL-CAA locus in the chloroplast genome. The designed primers were able to amplify only target species, enabling to distinguish the two closely related species with good sensitivity. Our results illustrated the ability of the method to identify lingonberry and American cranberry DNA using PCR without the need for probes or further sequencing. The dPCR method could also quantify the DNA copy number in mixed samples. Based on this study, the method provides a basis for a simple, fast, and sensitive quantitative authentication analysis of lingonberry and American cranberry by dPCR. Moreover, it can also provide a platform for authentication analyses of other plant species as well by utilizing the indel regions of chloroplast genomes.
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Affiliation(s)
- Katja Karppinen
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
| | - Anna Avetisyan
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Anne Linn Hykkerud
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, NO-9037 Tromsø, Norway; (K.K.); (A.A.)
- NIBIO, Norwegian Institute of Bioeconomy Research, Department of Horticulture, NO-1431 Ås, Norway;
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Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus. FORESTS 2022. [DOI: 10.3390/f13020265] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.
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Wu C, Deng C, Hilario E, Albert NW, Lafferty D, Grierson ERP, Plunkett BJ, Elborough C, Saei A, Günther CS, Ireland H, Yocca A, Edger PP, Jaakola L, Karppinen K, Grande A, Kylli R, Lehtola VP, Allan AC, Espley RV, Chagné D. A chromosome-scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition. Mol Ecol Resour 2021; 22:345-360. [PMID: 34260155 DOI: 10.1111/1755-0998.13467] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/22/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022]
Abstract
Bilberry (Vaccinium myrtillus L.) belongs to the Vaccinium genus, which includes blueberries (Vaccinium spp.) and cranberry (V. macrocarpon). Unlike its cultivated relatives, bilberry remains largely undomesticated, with berry harvesting almost entirely from the wild. As such, it represents an ideal target for genomic analysis, providing comparisons with the domesticated Vaccinium species. Bilberry is prized for its taste and health properties and has provided essential nutrition for Northern European indigenous populations. It contains high concentrations of phytonutrients, with perhaps the most important being the purple colored anthocyanins, found in both skin and flesh. Here, we present the first bilberry genome assembly, comprising 12 pseudochromosomes assembled using Oxford Nanopore (ONT) and Hi-C Technologies. The pseudochromosomes represent 96.6% complete BUSCO genes with an assessed LAI score of 16.3, showing a high conservation of synteny against the blueberry genome. Kmer analysis showed an unusual third peak, indicating the sequenced samples may have been from two individuals. The alternate alleles were purged so that the final assembly represents only one haplotype. A total of 36,404 genes were annotated after nearly 48% of the assembly was masked to remove repeats. To illustrate the genome quality, we describe the complex MYBA locus, and identify the key regulating MYB genes that determine anthocyanin production. The new bilberry genome builds on the genomic resources and knowledge of Vaccinium species, to help understand the genetics underpinning some of the quality attributes that breeding programs aspire to improve. The high conservation of synteny between bilberry and blueberry genomes means that comparative genome mapping can be applied to transfer knowledge about marker-trait association between these two species, as the loci involved in key characters are orthologous.
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Affiliation(s)
- Chen Wu
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand.,Genomics Aotearoa, Dunedin, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand.,Genomics Aotearoa, Dunedin, New Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand.,Genomics Aotearoa, Dunedin, New Zealand
| | | | - Declan Lafferty
- PFR, Palmerston North, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Blue J Plunkett
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Caitlin Elborough
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Ali Saei
- BioLumic Limited, Palmerston North, New Zealand
| | - Catrin S Günther
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Hilary Ireland
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - Alan Yocca
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA.,Department of Horticultural Science, Michigan State University, East Lansing, Michigan, USA
| | - Patrick P Edger
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Laura Jaakola
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, Tromsø, Norway.,NIBIO, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Katja Karppinen
- Department of Arctic and Marine Biology, UiT the Arctic University of Norway, Tromsø, Norway
| | | | - Ritva Kylli
- History, Culture and Communication studies, University of Oulu, Oulu, Finland
| | | | - Andrew C Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard V Espley
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Genomics Aotearoa, Dunedin, New Zealand.,PFR, Palmerston North, New Zealand
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