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Li Z, Liu J, Liang M, Guo Y, Chen X, Wu H, Jin S. De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing. BMC PLANT BIOLOGY 2024; 24:361. [PMID: 38702620 PMCID: PMC11069145 DOI: 10.1186/s12870-024-04978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. RESULTS PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. CONCLUSIONS We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.
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Affiliation(s)
- Ziwei Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiaxun Liu
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Mingtai Liang
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Yanbing Guo
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xia Chen
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Hongzhi Wu
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shoulin Jin
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Liu Z, Shen S, Wang Y, Sun S, Yu T, Fu Y, Zhou R, Li C, Cao R, Zhang Y, Li N, Sun L, Song X. The genome of Stephania japonica provides insights into the biosynthesis of cepharanthine. Cell Rep 2024; 43:113832. [PMID: 38381605 DOI: 10.1016/j.celrep.2024.113832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/28/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Stephania japonica is an early-diverging eudicotyledon plant with high levels of cepharanthine, proven to be effective in curing coronavirus infections. Here, we report a high-quality S. japonica genome. The genome size is 688.52 Mb, and 97.37% sequences anchor to 11 chromosomes. The genome comprises 67.46% repetitive sequences and 21,036 genes. It is closely related to two Ranunculaceae species, which diverged from their common ancestor 55.90-71.02 million years ago (Mya) with a whole-genome duplication 85.59-96.75 Mya. We further reconstruct ancestral karyotype of Ranunculales. Several cepharanthine biosynthesis genes are identified and verified by western blot. Two genes (Sja03G0243 and Sja03G0241) exhibit catalytic activity as shown by liquid chromatography-mass spectrometry. Then, cepharanthine biosynthesis genes, transcription factors, and CYP450 family genes are used to construct a comprehensive network. Finally, we construct an early-diverging eudicotyledonous genome resources (EEGR) database. As the first genome of the Menispermaceae family to be released, this study provides rich resources for genomic studies.
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Affiliation(s)
- Zhuo Liu
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Shaoqin Shen
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yujie Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Shuqi Sun
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Tong Yu
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yanhong Fu
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Rong Zhou
- Department of Food Science, Aarhus University, 8200 Aarhus, Denmark
| | - Chunjin Li
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Rui Cao
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yanshu Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Nan Li
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
| | - Liangdan Sun
- North China University of Science and Technology Affiliated Hospital, Tangshan 063000, China; Health Science Center, North China University of Science and Technology, Tangshan 063210, China; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology, Tangshan 063210, China; School of Public Health, North China University of Science and Technology, Tangshan 063210, China.
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan 063210, China.
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Liu Z, Fu Y, Wang H, Zhang Y, Han J, Wang Y, Shen S, Li C, Jiang M, Yang X, Song X. The high-quality sequencing of the Brassica rapa 'XiangQingCai' genome and exploration of genome evolution and genes related to volatile aroma. HORTICULTURE RESEARCH 2023; 10:uhad187. [PMID: 37899953 PMCID: PMC10611556 DOI: 10.1093/hr/uhad187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/08/2023] [Indexed: 10/31/2023]
Abstract
'Vanilla' (XQC, brassica variety chinensis) is an important vegetable crop in the Brassica family, named for its strong volatile fragrance. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assembled genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences were detected in the XQC genome, including 47 570 genes. Among all examined Brassicaceae species, XQC had the closest relationship with B. rapa QGC ('QingGengCai') and B. rapa Pakchoi. Two whole-genome duplication (WGD) events and one recent whole-genome triplication (WGT) event occurred in the XQC genome in addition to an ancient WGT event. The recent WGT was observed to occur during 21.59-24.40 Mya (after evolution rate corrections). Our findings indicate that XQC experienced gene losses and chromosome rearrangements during the genome evolution of XQC. The results of the integrated genomic and transcriptomic analyses revealed critical genes involved in the terpenoid biosynthesis pathway and terpene synthase (TPS) family genes. In summary, we determined a chromosome-level genome of B. rapa XQC and identified the key candidate genes involved in volatile fragrance synthesis. This work can act as a basis for the comparative and functional genomic analysis and molecular breeding of B. rapa in the future.
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Affiliation(s)
- Zhaokun Liu
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Yanhong Fu
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Huan Wang
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Yanping Zhang
- Suzhou Polytechnic Institute of Agriculture, Suzhou, Jiangsu 215008, China
| | - Jianjun Han
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Yingying Wang
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Shaoqin Shen
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Chunjin Li
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Mingmin Jiang
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Xuemei Yang
- Suzhou Academy of Agricultural Sciences, Suzhou, Jiangsu 215155, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
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Chen H, Zhang Y, Feng S. Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages. BMC Genomics 2023; 24:290. [PMID: 37254040 DOI: 10.1186/s12864-023-09389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages. RESULTS Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations. CONCLUSIONS This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yingchao Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Shuyan Feng
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
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Si C, Zhan D, Wang L, Sun X, Zhong Q, Yang S. Systematic Investigation of TCP Gene Family: Genome-Wide Identification and Light-Regulated Gene Expression Analysis in Pepino (Solanum Muricatum). Cells 2023; 12:cells12071015. [PMID: 37048089 PMCID: PMC10093338 DOI: 10.3390/cells12071015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of S. muricatum has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in S. muricatum using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in Arabidopsis thaliana; 40 of the 41 SmTCPs were localized to 12 chromosomes. In S. muricatum, 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for A. thaliana and S. muricatum were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.
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Affiliation(s)
- Cheng Si
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Deli Zhan
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Xuemei Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- Correspondence: (Q.Z.); (S.Y.)
| | - Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China; (C.S.); (D.Z.); (L.W.); (X.S.)
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Correspondence: (Q.Z.); (S.Y.)
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Shen S, Li N, Wang Y, Zhou R, Sun P, Lin H, Chen W, Yu T, Liu Z, Wang Z, Tan X, Zhu C, Feng S, Zhang Y, Song X. High-quality ice plant reference genome analysis provides insights into genome evolution and allows exploration of genes involved in the transition from C3 to CAM pathways. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2107-2122. [PMID: 35838009 PMCID: PMC9616530 DOI: 10.1111/pbi.13892] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/19/2022] [Accepted: 07/10/2022] [Indexed: 06/15/2023]
Abstract
Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high-quality chromosome-level ice plant genome sequence. This 98.05% genome sequence is anchored to nine chromosomes, with a total length of 377.97 Mb and an N50 scaffold of 40.45 Mb. Almost half of the genome (48.04%) is composed of repetitive sequences, and 24 234 genes have been annotated. Subsequent to the ancient whole-genome triplication (WGT) that occurred in eudicots, there has been no recent whole-genome duplication (WGD) or WGT in ice plants. However, we detected a novel WGT event that occurred in the same order in Simmondsia chinensis, which was previously overlooked. Our findings revealed that ice plants have undergone chromosome rearrangements and gene removal during evolution. Combined with transcriptome and comparative genomic data and expression verification, we identified several key genes involved in the CAM pathway and constructed a comprehensive network. As the first genome of the Aizoaceae family to be released, this report will provide a rich data resource for comparative and functional genomic studies of Aizoaceae, especially for studies on salt tolerance and C3-to-CAM transitions to improve crop yield and resistance.
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Affiliation(s)
- Shaoqin Shen
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Nan Li
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yujie Wang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Rong Zhou
- Department of Food ScienceAarhus UniversityAarhusDenmark
| | - Pengchuan Sun
- Key Laboratory for Bio‐Resource and Eco‐Environment of Ministry of Education, College of Life SciencesSichuan UniversityChengduChina
| | - Hao Lin
- School of Life Science and Technology and Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Wei Chen
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
- Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengduChina
| | - Tong Yu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhuo Liu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Zhiyuan Wang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Xiao Tan
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Changping Zhu
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Shuyan Feng
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yu Zhang
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
| | - Xiaoming Song
- College of Life Sciences/Center for Genomics and Bio‐computingNorth China University of Science and TechnologyTangshanHebeiChina
- School of Life Science and Technology and Center for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Food Science and Technology DepartmentUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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