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Jiang S, Zhang X, Yang X, Liu C, Wang L, Ma B, Miao Y, Hu J, Tan K, Wang Y, Jiang H, Wang J. A chromosome-level genome assembly of an early matured aromatic Japonica rice variety Qigeng10 to accelerate rice breeding for high grain quality in Northeast China. FRONTIERS IN PLANT SCIENCE 2023; 14:1134308. [PMID: 36909446 PMCID: PMC9995481 DOI: 10.3389/fpls.2023.1134308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Early-matured aromatic japonica rice from the Northeast is the most popular rice commodity in the Chinese market. The Qigeng10 (QG10) was one of the varieties with the largest planting area in this region in recent years. It was an early-matured japonica rice variety with a lot of superior traits such as semi-dwarf, lodging resistance, long grain, aromatic and good quality. Therefore, a high-quality assembly of Qigeng10 genome is critical and useful for japonica research and breeding. In this study, we produced a high-precision QG10 chromosome-level genome by using a combination of Nanopore and Hi-C platforms. Finally, we assembled the QG10 genome into 77 contigs with an N50 length of 11.80 Mb in 27 scaffolds with an N50 length of 30.55 Mb. The assembled genome size was 378.31Mb with 65 contigs and constituted approximately 99.59% of the 12 chromosomes. We identified a total of 1,080,819 SNPs and 682,392 InDels between QG10 and Nipponbare. We also annotated 57,599 genes by the Ab initio method, homology-based technique, and RNA-seq. Based on the assembled genome sequence, we detected the sequence variation in a total of 63 cloned genes involved in grain yield, grain size, disease tolerance, lodging resistance, fragrance, and many other important traits. Finally, we identified five elite alleles (qTGW2Nipponbare , qTGW3Nanyangzhan , GW5IR24 , GW6Suyunuo , and qGW8Basmati385 ) controlling long grain size, four elite alleles (COLD1Nipponbare , bZIP73Nipponbare , CTB4aKunmingxiaobaigu , and CTB2Kunmingxiaobaigu ) controlling cold tolerance, three non-functional alleles (DTH7Kitaake , Ghd7Hejiang19 , and Hd1Longgeng31 ) for early heading, two resistant alleles (PiaAkihikari and Pid4Digu ) for rice blast, a resistant allele STV11Kasalath for rice stripe virus, an NRT1.1BIR24 allele for higher nitrate absorption activity, an elite allele SCM3Chugoku117 for stronger culms, and the typical aromatic gene badh2-E2 for fragrance in QG10. These results not only help us to better elucidate the genetic mechanisms underlying excellent agronomic traits in QG10 but also have wide-ranging implications for genomics-assisted breeding in early-matured fragrant japonica rice.
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Affiliation(s)
- Shukun Jiang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Xijuan Zhang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianli Yang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chuanzeng Liu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Lizhi Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yi Miao
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Jifang Hu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Kefei Tan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yuxian Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Hui Jiang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Junhe Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Liang J, Kong L, Hu X, Fu C, Bai S. Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan. BMC PLANT BIOLOGY 2023; 23:94. [PMID: 36782126 PMCID: PMC9926808 DOI: 10.1186/s12870-023-04114-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The indica rice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice.
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Affiliation(s)
- Jiayan Liang
- Rice Research Institute Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Leilei Kong
- Rice Research Institute Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Xiaodan Hu
- Rice Research Institute Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Chongyun Fu
- Rice Research Institute Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Song Bai
- Rice Research Institute Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
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Fatimah S, Syafii M, Zulaeha S, Haristianita MD, Purwoko D. RNASeq data from Indonesian recalcitrant and non-recalcitrant rice varieties on anther culture. Data Brief 2022; 45:108760. [PMID: 36533293 PMCID: PMC9747646 DOI: 10.1016/j.dib.2022.108760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/24/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The assembly of dihaploid rice plants through anther culture was constrained due to the recalcitrant properties. A comprehensive investigation of gene expression patterns among rice varieties with recalcitrant and non-recalcitrant anthers will help to understand the cellular mechanisms and biological processes of recalcitrant properties in rice anther cultures. Therefore, we performed RNA sequencing and analysis on the anthers of three selected Indonesian rice varieties with opposite recalcitrant properties. The varieties are Fatmawati with non-recalcitrant properties, IR64 recalcitrant and Tarabas unknown. The Illumina NextSeq PE150 sequencer was used to generate a total crude nucleotide of approximately 41.21 Gb in size. From 272,239,682 total paired final raw reads, 137,343,391 total net reads were obtained and uploaded to NCBI's Sequence Read Archive (SRA) repository under BioProject accession number PRJNA856048. This dataset allowed us to identify and profile all expressed genes with functions associated with recalcitrant and non-recalcitrant properties. In addition, the transcriptome data obtained will be valuable for the discovery of potential gene markers and functional SNPs associated with functional traits to assist rice breeding programs through the development of Marker Assisted Selection (MAS).
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Affiliation(s)
- Siti Fatimah
- Agrotechnology Study Program, Faculty of Agriculture, Trunojoyo University, Unijoyo Campus, Telang, PO. BOX 2 Kamal – Bangkalan, East Java, Indonesia
| | - Mohammad Syafii
- Agrotechnology Study Program, Faculty of Agriculture, Trunojoyo University, Unijoyo Campus, Telang, PO. BOX 2 Kamal – Bangkalan, East Java, Indonesia
| | - Siti Zulaeha
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Building No. 630 PUSPIPTEK South Tangerang Banten 15314, Indonesia
| | | | - Devit Purwoko
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Building No. 630 PUSPIPTEK South Tangerang Banten 15314, Indonesia
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Lee YK, Lee Y, Jang S, Lee T, Woo MO, Seo J, Kim B, Koh HJ. Sequencing and de novo assembly of the Koshihikari genome and identification of the genomic region related to the eating quality of cooked rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:65. [PMID: 37309489 PMCID: PMC10248671 DOI: 10.1007/s11032-022-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/02/2022] [Indexed: 06/14/2023]
Abstract
The japonica rice (Oryza sativa L.) cultivar Koshihikari is considered an important breeding material with good eating quality (EQ). To effectively utilize Koshihikari in molecular breeding programs, determining its whole genome sequence including cultivar-specific segment is crucial. Here, the Koshihikari genome was sequenced using Nanopore and Illumina platforms, and de novo assembly was performed. A highly contiguous Koshihikari genome sequence was compared with Nipponbare, the reference genome of japonica. Genome-wide synteny was observed, as expected, without large structural variations. However, several gaps in alignment were detected on chromosomes 3, 4, 9, and 11. It was notable that previously identified EQ-related QTLs were found in these gaps. Moreover, sequence variations were identified in chromosome 11 at a region flanking the P5 marker, one of the significant markers of good EQ. The Koshihikari-specific P5 region was found to be transmitted through the lineage. High EQ cultivars derived from Koshihikari possessed P5 sequences; on the other hand, Koshihikari-derived low EQ cultivars didn't contain the P5 region, which implies that the P5 genomic region affects the EQ of Koshihikari progenies. The EQ of near-isogenic lines (NILs) of Samnam (a low EQ cultivar) genetic background harboring the P5 segment was improved compared to that of Samnam in Toyo taste value. The structure of the Koshihikari-specific P5 genomic region associated with good EQ was analyzed, which is expected to facilitate the molecular breeding of rice cultivars with superior EQ. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01335-3.
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Affiliation(s)
- Yoon Kyung Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yunjoo Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Su Jang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc, Seoul, 08511 Republic of Korea
| | - Mi-Ok Woo
- Science & Technology Policy Division, Ministry of Agriculture, Food and Rural Affairs, Sejong, South Korea
| | - Jeonghwan Seo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, 55365 Korea
| | - Backki Kim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Jong Koh
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Lu R, Liu J, Wang X, Song Z, Ji X, Li N, Ma G, Sun X. Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice. Int J Mol Sci 2022; 23:9705. [PMID: 36077110 PMCID: PMC9456513 DOI: 10.3390/ijms23179705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.
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Affiliation(s)
- Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jia Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Xuegang Wang
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Zhao Song
- Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Xiangdong Ji
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Naiwei Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Gang Ma
- Changshu Agricultural Science Research Institute, Changshu 215500, China
| | - Xiaoqin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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Kong W, Deng X, Liao Z, Wang Y, Zhou M, Wang Z, Li Y. De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:995634. [PMID: 36072319 PMCID: PMC9443666 DOI: 10.3389/fpls.2022.995634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Following the "green revolution," indica and japonica hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein de novo assembled the chromosome level genomes of an indica/xian rice (Luohui 9) and a japonica/geng rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (> F15) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, indica and Z7A, japonica). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, qKGW-6.1 and qKGW-8.1 were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (Ghd8) in qKGW-8.1 and qLH-KGW-8.1, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the People’s Republic of China, Nanchang, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Nishii K, Hart M, Kelso N, Barber S, Chen Y, Thomson M, Trivedi U, Twyford AD, Möller M. The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity. PLANT DIRECT 2022; 6:e388. [PMID: 35388373 PMCID: PMC8977575 DOI: 10.1002/pld3.388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 05/16/2023]
Abstract
Cape Primroses (Streptocarpus, Gesneriaceae) are an ideal study system for investigating the genetics underlying species diversity in angiosperms. Streptocarpus rexii has served as a model species for plant developmental research for over five decades due to its unusual extended meristem activity present in the leaves. In this study, we sequenced and assembled the complete nuclear, chloroplast, and mitochondrial genomes of S. rexii using Oxford Nanopore Technologies long read sequencing. Two flow cells of PromethION sequencing resulted in 32 billion reads and were sufficient to generate a draft assembly including the chloroplast, mitochondrial and nuclear genomes, spanning 776 Mbp. The final nuclear genome assembly contained 5,855 contigs, spanning 766 Mbp of the 929-Mbp haploid genome with an N50 of 3.7 Mbp and an L50 of 57 contigs. Over 70% of the draft genome was identified as repeats. A genome repeat library of Gesneriaceae was generated and used for genome annotation, with a total of 45,045 genes annotated in the S. rexii genome. Ks plots of the paranomes suggested a recent whole genome duplication event, shared between S. rexii and Primulina huaijiensis. A new chloroplast and mitochondrial genome assembly method, based on contig coverage and identification, was developed, and successfully used to assemble both organellar genomes of S. rexii. This method was developed into a pipeline and proved widely applicable. The nuclear genome of S. rexii and other datasets generated and reported here will be invaluable resources for further research to aid in the identification of genes involved in morphological variation underpinning plant diversification.
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Affiliation(s)
- Kanae Nishii
- Royal Botanic Garden EdinburghEdinburghUK
- Kanagawa UniversityHiratsukaJapan
| | | | | | | | - Yun‐Yu Chen
- Royal Botanic Garden EdinburghEdinburghUK
- Institute of Molecular Plant SciencesThe University of EdinburghEdinburghUK
| | - Marian Thomson
- Edinburgh Genomics, Ashworth LaboratoriesThe University of EdinburghEdinburghUK
| | - Urmi Trivedi
- Edinburgh Genomics, Ashworth LaboratoriesThe University of EdinburghEdinburghUK
| | - Alex D. Twyford
- Royal Botanic Garden EdinburghEdinburghUK
- Institute of Evolutionary Biology, Ashworth LaboratoriesThe University of EdinburghEdinburghUK
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Panibe JP, Wang L, Lee YC, Wang CS, Li WH. Identifying mutations in sd1, Pi54 and Pi-ta, and positively selected genes of TN1, the first semidwarf rice in Green Revolution. BOTANICAL STUDIES 2022; 63:9. [PMID: 35347474 PMCID: PMC8960516 DOI: 10.1186/s40529-022-00336-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Taichung Native 1 (TN1) is the first semidwarf rice cultivar that initiated the Green Revolution. As TN1 is a direct descendant of the Dee-geo-woo-gen cultivar, the source of the sd1 semidwarf gene, the sd1 gene can be defined through TN1. Also, TN1 is susceptible to the blast disease and is described as being drought-tolerant. However, genes related to these characteristics of TN1 are unknown. Our aim was to identify and characterize TN1 genes related to these traits. RESULTS Aligning the sd1 of TN1 to Nipponbare sd1, we found a 382-bp deletion including a frameshift mutation. Sanger sequencing validated this deleted region in sd1, and we proposed a model of the sd1 gene that corrects errors in the literature. We also predicted the blast disease resistant (R) genes of TN1. Orthologues of the R genes in Tetep, a well-known resistant cultivar that is commonly used as a donor for breeding new blast resistant cultivars, were then sought in TN1, and if they were present, we looked for mutations. The absence of Pi54, a well-known R gene, in TN1 partially explains why TN1 is more susceptible to blast than Tetep. We also scanned the TN1 genome using the PosiGene software and identified 11 genes deemed to have undergone positive selection. Some of them are associated with drought-resistance and stress response. CONCLUSIONS We have redefined the deletion of the sd1 gene in TN1, a direct descendant of the Dee-geo-woo-gen cultivar, and have corrected some literature errors. Moreover, we have identified blast resistant genes and positively selected genes, including genes that characterize TN1's blast susceptibility and abiotic stress response. These new findings increase the potential of using TN1 to breed new rice cultivars.
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Affiliation(s)
- Jerome P. Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 115 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 China
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung, 40227 Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300 Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
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Dai SF, Zhu XG, Hutang GR, Li JY, Tian JQ, Jiang XH, Zhang D, Gao LZ. Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza. FRONTIERS IN PLANT SCIENCE 2022; 13:921937. [PMID: 35874017 PMCID: PMC9301470 DOI: 10.3389/fpls.2022.921937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/16/2022] [Indexed: 05/08/2023]
Abstract
Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.
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Affiliation(s)
- Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xun-ge Zhu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ge-rang Hutang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-qi Tian
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xian-hui Jiang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Dan Zhang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Li-zhi Gao,
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Li K, Duan L, Zhang Y, Shi M, Chen S, Yang M, Ding Y, Peng Y, Dong Y, Yang H, Li Z, Zhang L, Fan Y, Ren M. Genome-wide identification and expression profile analysis of trihelix transcription factor family genes in response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:738. [PMID: 34649496 PMCID: PMC8515681 DOI: 10.1186/s12864-021-08000-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/08/2021] [Indexed: 12/04/2022] Open
Abstract
Background Transcription factors, including trihelix transcription factors, play vital roles in various growth and developmental processes and in abiotic stress responses in plants. The trihelix gene has been systematically studied in some dicots and monocots, including Arabidopsis, tomato, chrysanthemum, soybean, wheat, corn, rice, and buckwheat. However, there are no related studies on sorghum. Results In this study, a total of 40 sorghum trihelix (SbTH) genes were identified based on the sorghum genome, among which 34 were located in the nucleus, 5 in the chloroplast, 1 (SbTH38) in the cytoplasm, and 1 (SbTH23) in the extracellular membrane. Phylogenetic analysis of the SbTH genes and Arabidopsis and rice trihelix genes indicated that the genes were clustered into seven subfamilies: SIP1, GTγ, GT1, GT2, SH4, GTSb8, and orphan genes. The SbTH genes were located in nine chromosomes and none on chromosome 10. One pair of tandem duplication gene and seven pairs of segmental duplication genes were identified in the SbTH gene family. By qPCR, the expression of 14 SbTH members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. Except for the leaves in which the genes were upregulated after only 2 h exposure to high temperature, the 12 SbTH genes were significantly upregulated in the stems of sorghum seedlings after 24 h under the other abiotic stress conditions. Among the selected genes, SbTH10/37/39 were significantly upregulated, whereas SbTH32 was significantly downregulated under different stress conditions. Conclusions In this study, we identified 40 trihelix genes in sorghum and found that gene duplication was the main force driving trihelix gene evolution in sorghum. The findings of our study serve as a basis for further investigation of the functions of SbTH genes and providing candidate genes for stress-resistant sorghum breeding programmes and increasing sorghum yield. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08000-7.
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Affiliation(s)
- Kuiyin Li
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.,College of Agriculture, Anshun University, Anshun, 561000, People's Republic of China
| | - Lili Duan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yubo Zhang
- College of Agriculture, Anshun University, Anshun, 561000, People's Republic of China
| | - Miaoxiao Shi
- College of Agriculture, Anshun University, Anshun, 561000, People's Republic of China
| | - Songshu Chen
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, People's Republic of China
| | - Yashu Peng
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yabing Dong
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Zhenhua Li
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.,Guizhou Branch of National Wheat Improvement Center of Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, Guizhou, People's Republic of China
| | - Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China. .,Guizhou Branch of National Wheat Improvement Center of Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.
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11
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Panibe JP, Wang L, Li J, Li MY, Lee YC, Wang CS, Ku MSB, Lu MYJ, Li WH. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution. Genomics 2021; 113:2656-2674. [PMID: 34111524 DOI: 10.1016/j.ygeno.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 "miracle rice". We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.
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Affiliation(s)
- Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei 115, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210023 Nanjing, China
| | - Jengyi Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Chen Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Maurice S B Ku
- Department of Bioagricultutral Sciences, National Chiayi University, Chiayi 60004, Taiwan; School of Biological Sciences, Washington State University, Pullman 99164, WA, USA
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Hsiung Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
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Dumschott K, Schmidt MHW, Chawla HS, Snowdon R, Usadel B. Oxford Nanopore sequencing: new opportunities for plant genomics? JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5313-5322. [PMID: 32459850 PMCID: PMC7501810 DOI: 10.1093/jxb/eraa263] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 05/25/2020] [Indexed: 05/06/2023]
Abstract
DNA sequencing was dominated by Sanger's chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today's long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
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Affiliation(s)
- Kathryn Dumschott
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, Aachen, Germany
- IBG-4 Bioinformatics, CEPLAS, Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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