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Keefover-Ring K, Carlson CH, Hyden B, Azeem M, Smart LB. Genetic mapping of sexually dimorphic volatile and non-volatile floral secondary chemistry of a dioecious willow. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6352-6366. [PMID: 35710312 DOI: 10.1093/jxb/erac260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Secondary chemistry often differs between sexes in dioecious plant species, a pattern attributed to its possible role in the evolution and/or maintenance of dioecy. We used GC-MS to measure floral volatiles emitted from, and LC-MS to quantitate non-volatile secondary compounds contained in, female and male Salix purpurea willow catkins from an F2 family. Using the abundance of these chemicals, we then performed quantitative trait locus (QTL) mapping to locate them on the genome, identified biosynthetic candidate genes in the QTL intervals, and examined expression patterns of candidate genes using RNA-seq. Male flowers emitted more total terpenoids than females, but females produced more benzenoids. Male tissue contained greater amounts of phenolic glycosides, but females had more chalcones and flavonoids. A flavonoid pigment and a spermidine derivative were found only in males. Male catkins were almost twice the mass of females. Forty-two QTL were mapped for 25 chemical traits and catkin mass across 16 of the 19 S. purpurea chromosomes. Several candidate genes were identified, including a chalcone isomerase associated with seven compounds. A better understanding of the genetic basis of the sexually dimorphic chemistry of a dioecious species may shed light on how chemically mediated ecological interactions may have helped in the evolution and maintenance of dioecy.
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Affiliation(s)
- Ken Keefover-Ring
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Department of Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Muhammad Azeem
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
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2
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Choi BS, Choi SK, Kim NS, Choi IY. NBLAST: a graphical user interface-based two-way BLAST software with a dot plot viewer. Genomics Inform 2022; 20:e40. [PMID: 36239113 PMCID: PMC9576473 DOI: 10.5808/gi.21075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.
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Affiliation(s)
| | - Seon Kang Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Soo Kim
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
| | - Ik-Young Choi
- BIT Institute NBIT Co., Ltd., Chuncheon 24341, Korea
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
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3
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Wilkerson DG, Taskiran B, Carlson CH, Smart LB. Mapping the sex determination region in the Salix F1 hybrid common parent population confirms a ZW system in six diverse species. G3 GENES|GENOMES|GENETICS 2022; 12:6554199. [PMID: 35333299 PMCID: PMC9157088 DOI: 10.1093/g3journal/jkac071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/17/2022] [Indexed: 11/24/2022]
Abstract
Within the genus Salix, there are approximately 350 species native primarily to the northern hemisphere and adapted to a wide range of habitats. This diversity can be exploited to mine novel alleles conferring variation important for production as a bioenergy crop, but also to identify evolutionarily important genes, such as those involved in sex determination. To leverage this diversity, we created a mapping population by crossing 6 Salix species (Salix viminalis, Salix suchowensis, Salix integra, Salix koriyanagi, Salix udensis, and Salix alberti) to common male and female Salix purpurea parents. Each family was genotyped via genotyping-by-sequencing and assessed for kinship and population structure as well as the construction of 16 backcross linkage maps to be used as a genetic resource for breeding and selection. Analyses of population structure resolved both the parents and F1 progeny to their respective phylogenetic section and indicated that the S. alberti parent was misidentified and was most likely S.suchowensis. Sex determining regions were identified on Salix chromosome 15 in the female-informative maps for seven of the eight families indicating that these species share a common female heterogametic ZW sex system. The eighth family, S. integra × S. purpurea, was entirely female and had a truncated chromosome 15. Beyond sex determination, the Salix F1 hybrid common parent population (Salix F1 HCP) introduced here will be useful in characterizing genetic factors underlying complex traits, aid in marker-assisted selection, and support genome assemblies for this promising bioenergy crop.
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Affiliation(s)
- Dustin G Wilkerson
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Bircan Taskiran
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Sciences, Cornell University, Cornell AgriTech , Geneva, NY 14456, USA
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4
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Chaudhary P, Sharma PC. Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn ( Hippophae salicifolia). J Biomol Struct Dyn 2022; 41:2504-2517. [PMID: 35120412 DOI: 10.1080/07391102.2022.2034669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Seabuckthorn (Hippophae salicifolia) is a perennial, multipurpose wonder plant, popular for its immense medicinal, nutritional, and therapeutic properties. However, due to the lack of whole-genome-based studies, the molecular mechanism governing distinct sexual phenotypes is still not clear. We employed the high-throughput NGS Illumina NovaSeq paired-end technology to generate whole transcriptome profiles of male and female plants of H. salicifolia. In total, 3.2 million raw short reads were generated with an average length of 150 bp, including 50911358 reads from the male leaf tissue samples and 45850364 reads from the female leaf tissue samples. Clustering of the high-quality reads yielded de novo short read assembly of 50259 transcripts of >100 bp length. The final transcripts were assigned Gene Ontology (GO) terms. The digital expression of genes was studied using the DESeq2 of R package that identified 7180 differentially expressed genes (DEGs) between the male and female plant samples. Further, 10,850 simple sequence repeats, and 8,351 transcription factors, distributed in more than 85 transcription families, were also mined from the final assembled transcriptome. Next, COG and KEGG pathway analyses were performed to assign biological functional terms to the DEGs. The findings of the present study will provide a valuable resource for gene expression discovery and other functional genomics studies aiming towards the selection of candidate genes for the development of sex-specific markers in seabuckthorn and other closely related species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Parneeta Chaudhary
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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Hyden B, Carlson CH, Gouker FE, Schmutz J, Barry K, Lipzen A, Sharma A, Sandor L, Tuskan GA, Feng G, Olson MS, DiFazio SP, Smart LB. Integrative genomics reveals paths to sex dimorphism in Salix purpurea L. HORTICULTURE RESEARCH 2021; 8:170. [PMID: 34333534 PMCID: PMC8325687 DOI: 10.1038/s41438-021-00606-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 05/16/2023]
Abstract
Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.
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Affiliation(s)
- Brennan Hyden
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Fred E Gouker
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
- Floral and Nursery Plants Research Unit, US National Arboretum, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Aditi Sharma
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Guanqiao Feng
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Matthew S Olson
- Department of Biology, Texas Tech University, Lubbock, TX, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA.
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6
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Transcriptomic differences between male and female Trachycarpus fortunei. Sci Rep 2020; 10:12338. [PMID: 32704095 PMCID: PMC7378167 DOI: 10.1038/s41598-020-69107-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/01/2020] [Indexed: 11/09/2022] Open
Abstract
Trachycarpus fortunei (Hook.) is a typical dioecious plant, which has important economic value. There is currently no sex identification method for the early stages of T. fortunei growth. The aim of this study was to obtain expression and site differences between male and female T. fortunei transcriptomes. Using the Illumina sequencing platform, the transcriptomes of T. fortunei male and female plants were sequenced. By analyzing transcriptomic differences, the chromosomal helical binding protein (CHD1), serine/threonine protein kinase (STPK), cytochrome P450 716B1, and UPF0136 were found to be specifically expressed in T. fortunei males. After single nucleotide polymorphism (SNP) detection, a total of 12 male specific sites were found and the THUMP domain protein homologs were found to be male-biased expressed. Cytokinin dehydrogenase 6 (CKX6) was upregulated in male flowers and the lower concentrations of cytokinin (CTK) may be more conducive to male flower development. During new leaf growth, flavonoid and flavonol biosynthesis were initiated. Additionally, the flavonoids, 3',5'-hydroxylase (F3'5'H), flavonoids 3'-hydroxylase, were upregulated, which may cause the pale yellow phenotype. Based on these data, it can be concluded that inter-sex differentially expressed genes (DEGs) and specific SNP loci may be associated with sex determination in T. fortunei.
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Li J, Ye C. Genome-wide analysis of microsatellite and sex-linked marker identification in Gleditsia sinensis. BMC PLANT BIOLOGY 2020; 20:338. [PMID: 32680463 PMCID: PMC7367340 DOI: 10.1186/s12870-020-02551-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Gleditsia sinensis Lam. (Leguminosae), a dioecious perennial arbor, demonstrates important medicinal properties and economic value. These properties can be harnessed depending on the sex of the plant. However, the sex of the plants is difficult to identify accurately through morphological methods before the flowering. RESULTS We used bulked segregant analysis to screen sex-specific simple sequence repeat (SSR) markers in G. sinensis. Five male and five female plants were pooled to form the male and female bulks, respectively, and subjected to whole-genome sequencing. After high-throughput sequencing, 5,350,359 sequences were obtained, in which 2,065,210 SSRs were searched. Among them, the number of duplicated SSRs was the highest. The male plants could reach 857,874, which accounted for 60.86% of the total number of male plants. The female plants could reach 1,447,603, which accounted for 56.25% of the total model of the female plants. Among all the nucleotide repeat types, the A/T-rich motif was the most abundant. A total of 309,516 female strain-specific SSRs were selected by clustering. After designing the primers, the male and female gene pools were amplified, and five pairs of primers (i.e., 27, 34, 36, 39, and 41) were found to amplify the differential bands in the male and female gene pools. Using the five pairs of primers, we performed PCR verification on 10 individuals of known sex, which constructed the gene pool. The female plants amplified a single fragment of lengths (i.e., 186, 305, 266, 203, and 260 bp) and no male plant strip, thereby completing the identification of the male and female sexes of the G. sinensis. CONCLUSIONS This study provides accurate sex identification strategies between female and male plants, thus improving the utilization rate of G. sinensis resources.
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Affiliation(s)
- Jianjun Li
- College of Life Science, Henan Normal University, Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang, 453007 China
| | - Chenglin Ye
- College of Life Science, Henan Normal University, Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang, 453007 China
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8
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Pipatchartlearnwong K, Juntawong P, Wonnapinij P, Apisitwanich S, Vuttipongchaikij S. Towards sex identification of Asian Palmyra palm ( Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing. PeerJ 2019; 7:e7268. [PMID: 31333909 PMCID: PMC6626516 DOI: 10.7717/peerj.7268] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/06/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Asian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing. METHODS DNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries and de novo transcriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers. RESULTS Through extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Although de novo transcriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.
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Affiliation(s)
| | - Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
| | - Somsak Apisitwanich
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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Cossard GG, Toups MA, Pannell JR. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. ANNALS OF BOTANY 2019; 123:1119-1131. [PMID: 30289430 PMCID: PMC6612945 DOI: 10.1093/aob/mcy183] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/06/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species. METHODS The present study documents differences in gene expression in both above- and below-ground tissues of early pre-reproductive individuals of the wind-pollinated dioecious annual herb, Mercurialis annua, which otherwise shows clear sexual dimorphism only at the adult stage. KEY RESULTS Whereas males and females differed in their gene expression at the first leaf stage, sex-biased gene expression peaked just prior to, and after, flowering, as might be expected if sexual dimorphism is partly a response to differential costs of reproduction. Sex-biased genes were over-represented among putative sex-linked genes in M. annua but showed no evidence for more rapid evolution than unbiased genes. CONCLUSIONS Sex-biased gene expression in M. annua occurs as early as the first whorl of leaves is produced, is highly dynamic during plant development and varies substantially between vegetative tissues.
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Affiliation(s)
- Guillaume G Cossard
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
| | - Melissa A Toups
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - John R Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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10
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Zhao YJ, Liu XY, Guo R, Hu KR, Cao Y, Dai F. Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny. BMC Genomics 2019; 20:253. [PMID: 30925896 PMCID: PMC6440167 DOI: 10.1186/s12864-019-5627-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/20/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. RESULTS Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. CONCLUSIONS The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.
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Affiliation(s)
- You-jie Zhao
- Key Laboratory of Forestry and Ecological Big Data State Forestry Administration, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Xin-yi Liu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Ran Guo
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Kun-rong Hu
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Yong Cao
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
| | - Fei Dai
- College of Big data and Intelligent Engineering, Southwest Forestry University, Kunming, 650224 Yunnan People’s Republic of China
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11
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Sanderson BJ, Wang L, Tiffin P, Wu Z, Olson MS. Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera. THE NEW PHYTOLOGIST 2019; 221:527-539. [PMID: 30252135 DOI: 10.1111/nph.15421] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 06/29/2018] [Indexed: 05/11/2023]
Abstract
Because sexual dimorphism in plants is often less morphologically conspicuous than in animals, studies of sex-biased gene expression may provide a quantitative metric to better address their commonality, molecular pathways, consistency across tissues and taxa, and evolution. The presence of sex-biased gene expression in tissues other than the androecium or gynoecium, termed secondary sexual characters, suggests that these traits arose after the initial evolution of dioecy. Patterns of sequence evolution may provide evidence of positive selection that drove sexual specialization. We compared gene expression in male and female flowers and leaves of Populus balsamifera to assess the extent of sex-biased expression, and tested whether sex-biased genes exhibit elevated rates of protein evolution. Sex-biased expression was pervasive in floral tissue, but nearly absent in leaf tissue. Female-biased genes in flowers were associated with photosynthesis, whereas male-biased genes were associated with mitochondrial function. Sex-biased genes did not exhibit elevated rates of protein evolution, contrary to results from other studies in animals and plants. Our results suggest that the ecological and physiological constraints associated with the energetics of flowering, rather than sexual conflict, have probably shaped the differences in male and female gene expression in P. balsamifera.
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Affiliation(s)
- Brian J Sanderson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
| | - Li Wang
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St Paul, MN, 55108, USA
| | - Zhiqiang Wu
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409, USA
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12
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Bansal A, Salaria M, Sharma T, Stobdan T, Kant A. Comparative de novo transcriptome analysis of male and female Sea buckthorn. 3 Biotech 2018; 8:96. [PMID: 29430358 PMCID: PMC5796948 DOI: 10.1007/s13205-018-1122-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022] Open
Abstract
Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE (PKL), phytochrome-associated serine/threonine-protein phosphatase (FYPP), protein TOPLESS (TPL), sensitive to freezing 6 (SFR6), lysine-specific histone demethylase 1 homolog 1 (LDL1), pre-mRNA-processing-splicing factor 8A (PRP8A), sucrose synthase 4 (SUS4), ubiquitin carboxyl-terminal hydrolase 12 (UBP12), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.
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Affiliation(s)
- Ankush Bansal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234 India
| | - Mehul Salaria
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234 India
| | - Tashil Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234 India
| | - Tsering Stobdan
- Defence Institute of High Altitude Research, Defence R&D Organisation, Leh, Jammu and Kashmir India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh 173234 India
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Duan D, Jia Y, Yang J, Li ZH. Comparative Transcriptome Analysis of Male and Female Conelets and Development of Microsatellite Markers in Pinus bungeana, an Endemic Conifer in China. Genes (Basel) 2017; 8:genes8120393. [PMID: 29257091 PMCID: PMC5748711 DOI: 10.3390/genes8120393] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 02/02/2023] Open
Abstract
The sex determination in gymnosperms is still poorly characterized due to the lack of genomic/transcriptome resources and useful molecular genetic markers. To enhance our understanding of the molecular mechanisms of the determination of sexual recognition of reproductive structures in conifers, the transcriptome of male and female conelets were characterized in a Chinese endemic conifer species, Pinus bungeana Zucc. ex Endl. The 39.62 Gb high-throughput sequencing reads were obtained from two kinds of sexual conelets. After de novo assembly of the obtained reads, 85,305 unigenes were identified, 53,944 (63.23%) of which were annotated with public databases. A total of 12,073 differentially expressed genes were detected between the two types of sexes in P. bungeana, and 5766 (47.76%) of them were up-regulated in females. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched analysis suggested that some of the genes were significantly associated with the sex determination process of P. bungeana, such as those involved in tryptophan metabolism, zeatin biosynthesis, and cysteine and methionine metabolism, and the phenylpropanoid biosynthesis pathways. Meanwhile, some important plant hormone pathways (e.g., the gibberellin (GA) pathway, carotenoid biosynthesis, and brassinosteroid biosynthesis (BR) pathway) that affected sexual determination were also induced in P. bungeana. In addition, 8791 expressed sequence tag-simple sequence repeats (EST-SSRs) from 7859 unigenes were detected in P. bungeana. The most abundant repeat types were dinucleotides (1926), followed by trinucleotides (1711). The dominant classes of the sequence repeat were A/T (4942) in mononucleotides and AT/AT (1283) in dinucleotides. Among these EST-SSRs, 84 pairs of primers were randomly selected for the characterization of potential molecular genetic markers. Finally, 19 polymorphic EST-SSR primers were characterized. We found low to moderate levels of genetic diversity (NA = 1.754; HO = 0.206; HE = 0.205) across natural populations of P. bungeana. The cluster analysis revealed two distinct genetic groups for the six populations that were sampled in this endemic species, which might be caused by the fragmentation of habitats and long-term geographic isolation among different populations. Taken together, this work provides important insights into the molecular mechanisms of sexual identity in the reproductive organs of P. bungeana. The molecular genetic resources that were identified in this study will also facilitate further studies in functional genomics and population genetics in the Pinus species.
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Affiliation(s)
| | | | - Jie Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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14
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Wang W, Zhang X. Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses. Molecules 2017; 22:E2255. [PMID: 29258253 PMCID: PMC6149867 DOI: 10.3390/molecules22122255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/29/2017] [Accepted: 12/14/2017] [Indexed: 12/04/2022] Open
Abstract
Eucommia ulmoides is a model representative of the dioecious plants with sex differentiation at initiation. Nevertheless, the genetic mechanisms of sexual dimorphism and sex determination in E. ulmoides remain poorly understood. In this study de novo transcriptome sequencing on Illumina platform generated >45 billion high-quality bases from fresh leaves of six male and female individuals of E. ulmoides. A total of 148,595 unigenes with an average length of 801 base-pairs (bp) were assembled. Through comparative transcriptome analyses, 116 differentially expressed genes (DEGs) between the males and the females were detected, including 73 male-biased genes and 43 female-biased genes. Of these DEGs, three female-biased genes were annotated to be related with the sexually dimorphic gutta content in E. ulmoides. One male-biased DEG was identified as putative MADS box gene APETALA3, a B class floral organ identity gene in the flowering plants. SNPs calling analyses further confirmed that the APETALA3-like gene was probably involved in the sex determination in E. ulmoides. Four other male-biased DEGs were potential sex-associated genes as well with segregated SNPs in accord with sex type. In addition, the SNPs density was 1.02 per kilobase (kb) in the expressed genes of E. ulmoides, implying a relatively high genetic diversity.
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Affiliation(s)
- Wencai Wang
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, Guangzhou 510000, China.
| | - Xianzhi Zhang
- Department of Forestry Protection, College of Forestry, Northwest A&F University, Yangling 712100, China.
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Carlson CH, Choi Y, Chan AP, Serapiglia MJ, Town CD, Smart LB. Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome. Genome Biol Evol 2017; 9:2377-2394. [PMID: 28957462 PMCID: PMC5622329 DOI: 10.1093/gbe/evx174] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2017] [Indexed: 12/24/2022] Open
Abstract
The heritability of gene expression is critical in understanding heterosis and is dependent on allele-specific regulation by local and remote factors in the genome. We used RNA-Seq to test whether variation in gene expression among F1 and F2 intraspecific Salix purpurea progeny is attributable to cis- and trans-regulatory divergence. We assessed the mode of inheritance based on gene expression levels and allele-specific expression for F1 and F2 intraspecific progeny in two distinct tissue types: shoot tip and stem internode. In addition, we explored sexually dimorphic patterns of inheritance and regulatory divergence among F1 progeny individuals. We show that in S. purpurea intraspecific crosses, gene expression inheritance largely exhibits a maternal dominant pattern, regardless of tissue type or pedigree. A significantly greater number of cis- and trans-regulated genes coincided with upregulation of the maternal parent allele in the progeny, irrespective of the magnitude, whereas the paternal allele was higher expressed for genes showing cis × trans or compensatory regulation. Importantly, consistent with previous genetic mapping results for sex in shrub willow, we have delimited sex-biased gene expression to a 2 Mb pericentromeric region on S. purpurea chr15 and further refined the sex determination region. Altogether, our results offer insight into the inheritance of gene expression in S. purpurea as well as evidence of sexually dimorphic expression which may have contributed to the evolution of dioecy in Salix.
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Affiliation(s)
- Craig H. Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
| | - Yongwook Choi
- J. Craig Venter Institute, Rockville, Maryland 20850 USA
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland 20850 USA
| | - Michelle J. Serapiglia
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
| | | | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, New York 14456 USA
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16
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Li SF, Zhang GJ, Zhang XJ, Yuan JH, Deng CL, Gao WJ. Comparative transcriptome analysis reveals differentially expressed genes associated with sex expression in garden asparagus (Asparagus officinalis). BMC PLANT BIOLOGY 2017; 17:143. [PMID: 28830346 PMCID: PMC5567890 DOI: 10.1186/s12870-017-1091-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/14/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation in plants. However, the sex expression mechanisms in asparagus remain poorly understood. RESULTS De novo transcriptome sequencing via Illumina paired-end sequencing revealed more than 26 billion bases of high-quality sequence data from male and female asparagus flower buds. A total of 72,626 unigenes with an average length of 979 bp were assembled. In comparative transcriptome analysis, 4876 differentially expressed genes (DEGs) were identified in the possible sex-determining stage of female and male/supermale flower buds. Of these DEGs, 433, including 285 male/supermale-biased and 149 female-biased genes, were annotated as flower related. Of the male/supermale-biased flower-related genes, 102 were probably involved in anther development. In addition, 43 DEGs implicated in hormone response and biosynthesis putatively associated with sex expression and reproduction were discovered. Moreover, 128 transcription factor (TF)-related genes belonging to various families were found to be differentially expressed, and this finding implied the essential roles of TF in sex determination or differentiation in asparagus. Correlation analysis indicated that miRNA-DEG pairs were also implicated in asparagus sexual development. CONCLUSIONS Our study identified a large number of DEGs involved in the sex expression and reproduction of asparagus, including known genes participating in plant reproduction, plant hormone signaling, TF encoding, and genes with unclear functions. We also found that miRNAs might be involved in the sex differentiation process. Our study could provide a valuable basis for further investigations on the regulatory networks of sex determination and differentiation in asparagus and facilitate further genetic and genomic studies on this dioecious species.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Guo-Jun Zhang
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003 China
| | - Xue-Jin Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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17
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Detecting the Candidate Gender Determinants by Bioinformatic Prediction of miRNAs and Their Targets from Transcriptome Sequences of the Male and Female Flowers in Salix suchowensis. BIOMED RESEARCH INTERNATIONAL 2017. [PMID: 28638836 PMCID: PMC5468582 DOI: 10.1155/2017/9614596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
MicroRNAs (miRNAs) belong to a class of small, noncoding, and endogenous single-stranded RNAs that negatively regulate gene expression at the posttranscriptional level. Potential miRNAs can be identified based on sequence homology since miRNAs are highly conserved in plants. In this study, we aligned the expressed sequence tags derived from flower buds of male and female S. suchowensis to miRNAs in the miRBase, which enable us to identify 34 potential miRNAs from flower buds of the alternate sexes. Among them, 11 were from the female and 23 were from the male. Analyzing sequence complementarity led to identification of 124 and 55 miRNA targets in the male and female flower buds, respectively. By mapping the target genes of the predicted miRNAs to the sequence assemblies of S. suchowensis, a miR156 mediated gene was detected at the gender locus of willow, which was a transcription factor involved in flower development. It is noteworthy that this target is not expressed in male flower, while it is expressed fairly highly in female flower based on the transcriptome data derived from the alternate sexes of willows. This study provides new bioinformatic clue for further exploring the genetic mechanism underlying gender determination in willows.
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Ye N, Wang X, Li J, Bi C, Xu Y, Wu D, Ye Q. Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis. PeerJ 2017; 5:e3148. [PMID: 28367378 PMCID: PMC5374973 DOI: 10.7717/peerj.3148] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/05/2017] [Indexed: 11/20/2022] Open
Abstract
Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.
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Affiliation(s)
- Ning Ye
- College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China
| | - Xuelin Wang
- College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China
| | - Juan Li
- School of Electrical and Automatic Engineering, Nanjing Normal University , Nanjing , Jiangsu , China
| | - Changwei Bi
- School of Biological Science and Medical Engineering, Southeast University , Nanjing , Jiangsu , China
| | - Yiqing Xu
- College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China
| | - Dongyang Wu
- College of Forest Resources and Environment, Nanjing Forestry University , Nanjing , Jiangsu , China
| | - Qiaolin Ye
- College of Information Science and Technology, Nanjing Forestry University , Nanjing , Jiangsu , China
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Sobral R, Silva HG, Morais-Cecílio L, Costa MMR. The Quest for Molecular Regulation Underlying Unisexual Flower Development. FRONTIERS IN PLANT SCIENCE 2016; 7:160. [PMID: 26925078 PMCID: PMC4759290 DOI: 10.3389/fpls.2016.00160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/30/2016] [Indexed: 05/16/2023]
Abstract
The understanding of the molecular mechanisms responsible for the making of a unisexual flower has been a long-standing quest in plant biology. Plants with male and female flowers can be divided mainly into two categories: dioecious and monoecious, and both sexual systems co-exist in nature in ca of 10% of the angiosperms. The establishment of male and female traits has been extensively described in a hermaphroditic flower and requires the interplay of networks, directly and indirectly related to the floral organ identity genes including hormonal regulators, transcription factors, microRNAs, and chromatin-modifying proteins. Recent transcriptomic studies have been uncovering the molecular processes underlying the establishment of unisexual flowers and there are many parallelisms between monoecious, dioecious, and hermaphroditic individuals. Here, we review the paper entitled "Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber" published in 2014 in the Frontiers of Plant Science (volume 5 |Article 599) and discussed it in the context of recent studies with other dioecious and monoecious plants that utilized high-throughput platforms to obtain transcriptomic profiles of male and female unisexual flowers. In some unisexual flowers, the developmental programs that control organ initiation fail and male or female organs do not form, whereas in other species, organ initiation and development occur but they abort or arrest during different species-specific stages of differentiation. Therefore, a direct comparison of the pathways responsible for the establishment of unisexual flowers in different species are likely to reveal conserved modules of gene regulatory hubs involved in stamen or carpel development, as well as differences that reflect the different stages of development in which male and/or female organ arrest or loss-of-function occurs.
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Affiliation(s)
- Rómulo Sobral
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Helena G. Silva
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
| | - Leonor Morais-Cecílio
- Departamento de Recursos Naturais Ambiente e Território, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de LisboaLisboa, Portugal
| | - Maria M. R. Costa
- Biosystems and Integrative Sciences Institute, Plant Functional Biology Centre, University of MinhoBraga, Portugal
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20
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Chen Y, Wang T, Fang L, Li X, Yin T. Confirmation of Single-Locus Sex Determination and Female Heterogamety in Willow Based on Linkage Analysis. PLoS One 2016; 11:e0147671. [PMID: 26828940 PMCID: PMC4734660 DOI: 10.1371/journal.pone.0147671] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/06/2016] [Indexed: 01/02/2023] Open
Abstract
In this study, we constructed high-density genetic maps of Salix suchowensis and mapped the gender locus with an F1 pedigree. Genetic maps were separately constructed for the maternal and paternal parents by using amplified fragment length polymorphism (AFLP) markers and the pseudo-testcross strategy. The maternal map consisted of 20 linkage groups that spanned a genetic distance of 2333.3 cM; whereas the paternal map contained 21 linkage groups that covered 2260 cM. Based on the established genetic maps, it was found that the gender of willow was determined by a single locus on linkage group LG_03, and the female was the heterogametic gender. Aligned with mapped SSR markers, linkage group LG_03 was found to be associated with chromosome XV in willow. It is noteworthy that marker density in the vicinity of the gender locus was significantly higher than that expected by chance alone, which indicates severe recombination suppression around the gender locus. In conclusion, this study confirmed the findings on the single-locus sex determination and female heterogamety in willow. It also provided additional evidence that validated the previous studies, which found that different autosomes evolved into sex chromosomes between the sister genera of Salix (willow) and Populus (poplar).
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Affiliation(s)
- Yingnan Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tiantian Wang
- Forestry Research Institute of Jingdezhen, Jiangxi, China
| | - Lecheng Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiaoping Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
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Allwright MR, Taylor G. Molecular Breeding for Improved Second Generation Bioenergy Crops. TRENDS IN PLANT SCIENCE 2016; 21:43-54. [PMID: 26541073 DOI: 10.1016/j.tplants.2015.10.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 09/18/2015] [Accepted: 10/02/2015] [Indexed: 05/24/2023]
Abstract
There is increasing urgency to develop and deploy sustainable sources of energy to reduce our global dependency on finite, high-carbon fossil fuels. Lignocellulosic feedstocks, used in power and liquid fuel generation, are valuable sources of non-food plant biomass. They are cultivated with minimal inputs on marginal or degraded lands to prevent competition with arable agriculture and offer significant potential for sustainable intensification (the improvement of yield without the necessity for additional inputs) through advanced molecular breeding. This article explores progress made in next generation sequencing, advanced genotyping, association genetics, and genetic modification in second generation bioenergy production. Using poplar as an exemplar where most progress has been made, a suite of target traits is also identified giving insight into possible routes for crop improvement and deployment in the immediate future.
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Affiliation(s)
- Mike R Allwright
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, SO17 1BJ Southampton, UK
| | - Gail Taylor
- Centre for Biological Sciences, Life Sciences Building, University of Southampton, SO17 1BJ Southampton, UK.
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Du S, Sang Y, Liu X, Xing S, Li J, Tang H, Sun L. Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L. FRONTIERS IN PLANT SCIENCE 2016; 7:871. [PMID: 27379148 PMCID: PMC4910463 DOI: 10.3389/fpls.2016.00871] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/02/2016] [Indexed: 05/21/2023]
Abstract
In plants, sex determination is a comprehensive process of correlated events, which involves genes that are differentially and/or specifically expressed in distinct developmental phases. Exploring gene expression profiles from different sex types will contribute to fully understanding sex determination in plants. In this study, we conducted RNA-sequencing of female and male buds (FB and MB) as well as ovulate strobilus and staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the genes potentially related to sex determination in this species. Approximately 60 Gb of clean reads were obtained from eight cDNA libraries. De novo assembly of the clean reads generated 108,307 unigenes with an average length of 796 bp. Among these unigenes, 51,953 (47.97%) had at least one significant match with a gene sequence in the public databases searched. A total of 4709 and 9802 differentially expressed genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively. Genes involved in plant hormone signal and transduction as well as those encoding DNA methyltransferase were found to be differentially expressed between different sex types. Their potential roles in sex determination of G. biloba were discussed. Pistil-related genes were expressed in male buds while anther-specific genes were identified in female buds, suggesting that dioecism in G. biloba was resulted from the selective arrest of reproductive primordia. High correlation of expression level was found between the RNA-Seq and quantitative real-time PCR results. The transcriptome resources that we generated allowed us to characterize gene expression profiles and examine differential expression profiles, which provided foundations for identifying functional genes associated with sex determination in G. biloba.
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Yang J, Li K, Zheng W, Zhang H, Cao X, Lan Y, Yang C, Li C. Characterization of early transcriptional responses to cadmium in the root and leaf of Cd-resistant Salix matsudana Koidz. BMC Genomics 2015; 16:705. [PMID: 26381125 PMCID: PMC4573677 DOI: 10.1186/s12864-015-1923-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salix matsudana Koidz. is a fast growing tree species. It has a high cadmium (Cd) tolerance capacity, making it potentially suitable for phytoremediation. Presently, transcriptomic and physiological Cd response mechanisms are poorly understood. Transcriptomic analysis in early response to high (50 μM) Cd levels was investigated in leaf and root of Cd-resistant S. matsudana Koidz.. RESULTS Analysis of the response profiles demonstrate the existence of a complex transcriptional network in the root and leaf when exposed to Cd. The main response in the root involved up-regulation of genes associated with defence response via callose deposition in the cell wall and cell wall thickening. In the leaf, transcripts related to biotic stress signalling and secondary metabolism were activated. Additionally, many lignin and brassinosteroids synthesis pathway genes were induced mainly in the leaf, indicating that gene response to Cd was tissue-specific. The Cd transcriptome results were consistent with observed physiological changes. CONCLUSION The sub-localization, transcriptional network, and physiological regulation demonstrate the tissue-specific manner of Cd response, and provide a novel insight into in early response of tree species to Cd exposure.
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Affiliation(s)
- Jingli Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Kun Li
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Wei Zheng
- Research Center on Life Sciences and Environmental Sciences, Harbin University of Commerce, Harbin, 150076, China.
| | - Haizhen Zhang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Xudong Cao
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Yunxiang Lan
- School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Chuanping Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Chawla A, Stobdan T, Srivastava RB, Jaiswal V, Chauhan RS, Kant A. Sex-Biased Temporal Gene Expression in Male and Female Floral Buds of Seabuckthorn (Hippophae rhamnoides). PLoS One 2015; 10:e0124890. [PMID: 25915052 PMCID: PMC4410991 DOI: 10.1371/journal.pone.0124890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 03/18/2015] [Indexed: 12/29/2022] Open
Abstract
Seabuckthorn is an economically important dioecious plant in which mechanism of sex determination is unknown. The study was conducted to identify seabuckthorn homologous genes involved in floral development which may have role in sex determination. Forty four putative Genes involved in sex determination (GISD) reported in model plants were shortlisted from literature survey, and twenty nine seabuckthorn homologous sequences were identified from available seabuckthorn genomic resources. Of these, 21 genes were found to differentially express in either male or female flower bud stages. HrCRY2 was significantly expressed in female flower buds only while HrCO had significant expression in male flowers only. Among the three male and female floral development stages (FDS), male stage II had significant expression of most of the GISD. Information on these sex-specific expressed genes will help in elucidating sex determination mechanism in seabuckthorn.
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Affiliation(s)
- Aseem Chawla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Tsering Stobdan
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Ravi B. Srivastava
- Defence Institute of High Altitude Research, Defence R & D Organisation, Leh, Jammu, and Kashmir, India
| | - Varun Jaiswal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Rajinder S. Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
- * E-mail:
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Yang L, Gong F, Xiong E, Wang W. Proteomics: a promising tool for research on sex-related differences in dioecious plants. FRONTIERS IN PLANT SCIENCE 2015; 6:954. [PMID: 26583026 PMCID: PMC4631940 DOI: 10.3389/fpls.2015.00954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/19/2015] [Indexed: 05/07/2023]
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Identification and expression analysis of salt-responsive genes using a comparative microarray approach in Salix matsudana. Mol Biol Rep 2014; 41:6555-68. [DOI: 10.1007/s11033-014-3539-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
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Chen Y, Mao Y, Liu H, Yu F, Li S, Yin T. Transcriptome analysis of differentially expressed genes relevant to variegation in peach flowers. PLoS One 2014; 9:e90842. [PMID: 24603808 PMCID: PMC3948169 DOI: 10.1371/journal.pone.0090842] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 02/06/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Variegation in flower color is commonly observed in many plant species and also occurs on ornamental peaches (Prunus persica f. versicolor [Sieb.] Voss). Variegated plants are highly valuable in the floricultural market. To gain a global perspective on genes differentially expressed in variegated peach flowers, we performed large-scale transcriptome sequencing of white and red petals separately collected from a variegated peach tree. RESULTS A total of 1,556,597 high-quality reads were obtained, with an average read length of 445 bp. The ESTs were assembled into 16,530 contigs and 42,050 singletons. The resulting unigenes covered about 60% of total predicted genes in the peach genome. These unigenes were further subjected to functional annotation and biochemical pathway analysis. Digital expression analysis identified a total of 514 genes differentially expressed between red and white flower petals. Since peach flower coloration is determined by the expression and regulation of structural genes relevant to flavonoid biosynthesis, a detailed examination detected four key structural genes, including C4H, CHS, CHI and F3H, expressed at a significantly higher level in red than in white petal. Except for the structural genes, we also detected 11 differentially expressed regulatory genes relating to flavonoid biosynthesis. Using the differentially expressed structural genes as the test objects, we validated the digital expression results by using quantitative real-time PCR, and the differential expression of C4H, CHS and F3H were confirmed. CONCLUSION In this study, we generated a large EST collection from flower petals of a variegated peach. By digital expression analysis, we identified an informative list of candidate genes associated with variegation in peach flowers, which offered a unique opportunity to uncover the genetic mechanisms underlying flower color variegation.
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Affiliation(s)
- Yingnan Chen
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yan Mao
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hailin Liu
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Faxin Yu
- Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, China
| | - Shuxian Li
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tongming Yin
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, Jiangsu, China
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De novo assembly and characterization of Sophora japonica transcriptome using RNA-seq. BIOMED RESEARCH INTERNATIONAL 2014; 2014:750961. [PMID: 24516854 PMCID: PMC3910276 DOI: 10.1155/2014/750961] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/22/2013] [Accepted: 11/25/2013] [Indexed: 11/17/2022]
Abstract
Sophora japonica Linn (Chinese Scholar Tree) is a shrub species belonging to the subfamily Faboideae of the pea family Fabaceae. In this study, RNA sequencing of S. japonica transcriptome was performed to produce large expression datasets for functional genomic analysis. Approximate 86.1 million high-quality clean reads were generated and assembled de novo into 143010 unique transcripts and 57614 unigenes. The average length of unigenes was 901 bps with an N50 of 545 bps. Four public databases, including the NCBI nonredundant protein (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Cluster of Orthologous Groups (COG), were used to annotate unigenes through NCBI BLAST procedure. A total of 27541 of 57614 unigenes (47.8%) were annotated for gene descriptions, conserved protein domains, or gene ontology. Moreover, an interaction network of unigenes in S. japonica was predicted based on known protein-protein interactions of putative orthologs of well-studied plant genomes. The transcriptome data of S. japonica reported here represents first genome-scale investigation of gene expressions in Faboideae plants. We expect that our study will provide a useful resource for further studies on gene expression, genomics, functional genomics, and protein-protein interaction in S. japonica.
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Zhou H, Cheng FY, Wang R, Zhong Y, He C. Transcriptome comparison reveals key candidate genes responsible for the unusual reblooming trait in tree peonies. PLoS One 2013; 8:e79996. [PMID: 24244590 PMCID: PMC3828231 DOI: 10.1371/journal.pone.0079996] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/29/2013] [Indexed: 11/19/2022] Open
Abstract
Tree peonies are important ornamental plants worldwide, but growing them can be frustrating due to their short and concentrated flowering period. Certain cultivars exhibit a reblooming trait that provides a valuable alternative for extending the flowering period. However, the genetic control of reblooming in tree peonies is not well understood. In this study, we compared the molecular properties and morphology of reblooming and non-reblooming tree peonies during the floral initiation and developmental processes. Using transcriptome sequencing technology, we generated 59,275 and 63,962 unigenes with a mean size of 698 bp and 699 bp from the two types of tree peonies, respectively, and identified eight differentially expressed genes that are involved in the floral pathways of Arabidopsis thaliana. These differentially regulated genes were verified through a detailed analysis of their expression pattern during the floral process by real time RT-PCR. From this combined analysis, we identified four genes, PsFT, PsVIN3, PsCO and PsGA20OX, which likely play important roles in the regulation of the reblooming process in tree peonies. These data constitute a valuable resource for the discovery of genes involved in flowering time and insights into the molecular mechanism of flowering to further accelerate the breeding of tree peonies and other perennial woody plants.
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Affiliation(s)
- Hua Zhou
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Center, Beijing, China
- Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang, China
| | - Fang-Yun Cheng
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Center, Beijing, China
- * E-mail: (FYC); (CYH)
| | - Rong Wang
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Center, Beijing, China
| | - Yuan Zhong
- Landscape Architecture College of Beijing Forestry University, National Flower Engineering Research Center, Beijing, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (FYC); (CYH)
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