1
|
Wang W, Duan J, Wang X, Feng X, Chen L, Clark CB, Swarm SA, Wang J, Lin S, Nelson RL, Meyers BC, Feng X, Ma J. Long noncoding RNAs underlie multiple domestication traits and leafhopper resistance in soybean. Nat Genet 2024; 56:1270-1277. [PMID: 38684899 DOI: 10.1038/s41588-024-01738-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
The origin and functionality of long noncoding RNA (lncRNA) remain poorly understood. Here, we show that multiple quantitative trait loci modulating distinct domestication traits in soybeans are pleiotropic effects of a locus composed of two tandem lncRNA genes. These lncRNA genes, each containing two inverted repeats, originating from coding sequences of the MYB genes, function in wild soybeans by generating clusters of small RNA (sRNA) species that inhibit the expression of their MYB gene relatives through post-transcriptional regulation. By contrast, the expression of lncRNA genes in cultivated soybeans is severely repressed, and, consequently, the corresponding MYB genes are highly expressed, shaping multiple distinct domestication traits as well as leafhopper resistance. The inverted repeats were formed before the divergence of the Glycine genus from the Phaseolus-Vigna lineage and exhibit strong structure-function constraints. This study exemplifies a type of target for selection during plant domestication and identifies mechanisms of lncRNA formation and action.
Collapse
Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jingbo Duan
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xingxing Feng
- Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Stephen A Swarm
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beck's Hybrids, Atlanta, IN, USA
| | - Jinbin Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Sen Lin
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Randall L Nelson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Blake C Meyers
- Genome Center and Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Xianzhong Feng
- Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
2
|
Lin RC, Ferreira BT, Yuan YW. The molecular basis of phenotypic evolution: beyond the usual suspects. Trends Genet 2024:S0168-9525(24)00097-0. [PMID: 38704304 DOI: 10.1016/j.tig.2024.04.010] [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: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
It has been well documented that mutations in coding DNA or cis-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many 'unusual suspects' in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the 'grandeur of life'.
Collapse
Affiliation(s)
- Rong-Chien Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Bianca T Ferreira
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA.
| |
Collapse
|
3
|
Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
Collapse
Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
| |
Collapse
|
4
|
Gultyaev AP, Koster C, van Batenburg DC, Sistermans T, van Belle N, Vijfvinkel D, Roussis A. Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements. NAR Genom Bioinform 2023; 5:lqad091. [PMID: 37850034 PMCID: PMC10578108 DOI: 10.1093/nargab/lqad091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023] Open
Abstract
Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.
Collapse
Affiliation(s)
- Alexander P Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Department of Viroscience, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Celine Koster
- Life Science & Technology Honours College, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
- Amsterdam University Medical Center, Department of Human Genetics, section Ophthalmogenetics, Location AMC, Meibergdreef 9, Amsterdam, The Netherlands
| | - Diederik Cames van Batenburg
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- CareRate, Unit E1.165, Stationsplein 45, 3013 AK Rotterdam, The Netherlands
| | - Tom Sistermans
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Niels van Belle
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Daan Vijfvinkel
- Leiden Institute of Advanced Computer Science, Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Andreas Roussis
- National & Kapodistrian University of Athens, Faculty of Biology, Section of Botany, Group Molecular Plant Physiology, Panepistimiopolis - Zografou - Athens, 15784, Greece
| |
Collapse
|
5
|
Lim SH, Kim DH, Lee JY. Molecular mechanism controlling anthocyanin composition and content in radish plants with different root colors. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108091. [PMID: 37864927 DOI: 10.1016/j.plaphy.2023.108091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Radish (Raphanus sativus) roots exhibit various colors that reflect their anthocyanin compositions and contents. However, the details of the mechanism linking the expression of anthocyanin biosynthesis and their transcriptional regulators to anthocyanin composition in radish roots remained unknown. Here, we characterized the role of the anthocyanin biosynthetic enzyme flavonoid 3'-hydroxylase (RsF3'H), together with the R2R3 MYB transcription factor (TF) RsMYB1 and the basic helix-loop-helix (bHLH) TF TRANSPARENT TESTA 8 (RsTT8), in four radish plants with different root colors: white (W), deep red (DR), dark purple (DP), and dark greyish purple (DGP). The DR plant contained heterozygous for RsF3'H with low expression level and accumulated a large amount of pelargonidin, resulting in deep red color. While, the DP and DGP plants accumulated the cyanidin due to the higher expression level of functional RsF3'H. Notably, RsMYB1 and RsTT8 transcripts were abundant in all pigmented roots, but not in white roots. To investigate the differential expression of RsMYB1 and RsTT8, we compared the sequences of their promoter regions among the four radish plants, revealing variations in the numbers of cis-elements and in promoter architecture. Promoter activation assays demonstrated that variation in the RsMYB1 and RsTT8 promoters may contribute to the expression level of these genes, and RsMYB1 can activate its own expression as well as promote the RsTT8 expression. These results suggested that RsF3'H plays a vital role in anthocyanin composition and the expression level of both RsMYB1 and RsTT8 are crucial determinants for anthocyanin content in radish roots. Overall, these findings provide insight into the molecular basis of anthocyanin composition and level in radish roots.
Collapse
Affiliation(s)
- Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Republic of Korea; Research Institute of International Technology and Information, Hankyong National University, Anseong, 17579, Republic of Korea.
| | - Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Republic of Korea; Research Institute of International Technology and Information, Hankyong National University, Anseong, 17579, Republic of Korea
| | - Jong-Yeol Lee
- National Academy of Agricultural Science, Rural Development Administration, Jeonju, 54874, Republic of Korea
| |
Collapse
|
6
|
Gorbenko IV, Petrushin IS, Shcherban AB, Orlov YL, Konstantinov YM. Short Interrupted Repeat Cassette (SIRC)-Novel Type of Repetitive DNA Element Found in Arabidopsis thaliana. Int J Mol Sci 2023; 24:11116. [PMID: 37446293 DOI: 10.3390/ijms241311116] [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: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Short interrupted repeat cassette (SIRC)-a novel DNA element found throughout the A. thaliana nuclear genome. SIRCs are represented by short direct repeats interrupted by diverse DNA sequences. The maxima of SIRC's distribution are located within pericentromeric regions. We suggest that originally SIRC was a special case of the complex internal structure of the miniature inverted repeat transposable element (MITE), and further MITE amplification, transposition, and loss of terminal inverted repeats gave rise to SIRC as an independent DNA element. SIRC sites were significantly enriched with several histone modifications associated with constitutive heterochromatin and mobile genetic elements. The majority of DNA-binding proteins, strongly associated with SIRC, are related to histone modifications for transcription repression. A part of SIRC was found to overlap highly inducible protein-coding genes, suggesting a possible regulatory role for these elements, yet their definitive functions need further investigation.
Collapse
Affiliation(s)
- Igor V Gorbenko
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
| | - Ivan S Petrushin
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Department of Business Communications and Informatics, Irkutsk State University, Irkutsk 664033, Russia
| | - Andrey B Shcherban
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
- Kurchatov Genomic Center ICG SB RAS, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
- Agrarian and Technological Institute, Peoples' Friendship University of Russia, Moscow 117198, Russia
| | - Yuri M Konstantinov
- Cell Biology and Bioengineering, Siberian Institute of Plant Physiology and Biochemistry SB RAS, Irkutsk 664033, Russia
- Biosoil Department, Irkutsk State University, Irkutsk 664003, Russia
| |
Collapse
|