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Ferreira-Neto JRC, da Silva MD, Binneck E, de Melo NF, da Silva RH, de Melo ALTM, Pandolfi V, Bustamante FDO, Brasileiro-Vidal AC, Benko-Iseppon AM. Bridging the Gap: Combining Genomics and Transcriptomics Approaches to Understand Stylosanthes scabra, an Orphan Legume from the Brazilian Caatinga. PLANTS (BASEL, SWITZERLAND) 2023; 12:3246. [PMID: 37765410 PMCID: PMC10535828 DOI: 10.3390/plants12183246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Stylosanthes scabra is a scientifically orphaned legume found in the Brazilian Caatinga biome (a semi-arid environment). This work utilized omics approaches to investigate some ecophysiological aspects of stress tolerance/resistance in S. scabra, study its genomic landscape, and predict potential metabolic pathways. Considering its high-confidence conceptual proteome, 1694 (~2.6%) proteins were associated with resistance proteins, some of which were found in soybean QTL regions that confer resistance to Asian soybean rust. S. scabra was also found to be a potential source of terpenes, as biosynthetic gene clusters associated with terpene biosynthesis were identified in its genome. The analysis revealed that mobile elements comprised approximately 59% of the sequenced genome. In the remaining 41% of the sections, some of the 22,681 protein-coding gene families were categorized into two informational groups: those that were specific to S. scabra and those that expanded significantly compared to their immediate ancestor. Biological process enrichment analyses indicated that these gene families play fundamental roles in the adaptation of S. scabra to extreme environments. Additionally, phylogenomic analysis indicated a close evolutionary relationship between the genera Stylosanthes and Arachis. Finally, this study found a high number (57) of aquaporin-encoding loci in the S. scabra genome. RNA-Seq and qPCR data suggested that the PIP subfamily may play a key role in the species' adaptation to water deficit conditions. Overall, these results provide valuable insights into S. scabra biology and a wealth of gene/transcript information for future legume omics studies.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil;
| | - Eliseu Binneck
- Brazilian Agricultural Research Corporation’s—EMBRAPA Soybean, Rodovia Carlos João Strass—Distrito de Warta, Londrina 86001-970, PR, Brazil;
| | - Natoniel Franklin de Melo
- Brazilian Agricultural Research Corporation’s—EMBRAPA Semiárido, Rodovia BR-428, Km 152, s/n-Zona Rural, Petrolina 56302-970, PE, Brazil;
| | - Rahisa Helena da Silva
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Ana Luiza Trajano Mangueira de Melo
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Fernanda de Oliveira Bustamante
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Ana Christina Brasileiro-Vidal
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
| | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Center of Biosciences, Genetics Department, Federal University of Pernambuco, Av. Prof. Moraes Rego, 1235, Recife 50670-901, PE, Brazil; (R.H.d.S.); (A.L.T.M.d.M.); (V.P.); (F.d.O.B.); (A.C.B.-V.)
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Oliveira MAS, Nunes T, Dos Santos MA, Ferreira Gomes D, Costa I, Van-Lume B, Marques Da Silva SS, Oliveira RS, Simon MF, Lima GSA, Gissi DS, Almeida CCDS, Souza G, Marques A. High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae). Front Genet 2021; 12:727314. [PMID: 34630521 PMCID: PMC8495327 DOI: 10.3389/fgene.2021.727314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.
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Affiliation(s)
| | - Tomáz Nunes
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | | | | | - Iara Costa
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | | | - Ronaldo Simão Oliveira
- Campus Xique Xique, Federal Institute of Education, Science and Technology of Bahia, Xique-Xique, Brazil
| | | | - Gaus S A Lima
- Center of Agronomic Sciences, Federal University of Alagoas, Rio Largo, Brazil
| | - Danilo Soares Gissi
- Department of Biostatistics, Institute of Biosciences-IBB, Plant Biology, Parasitology and Zoology, São Paulo State University-UNESP, Botucatu, Brazil
| | | | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Federal University of Pernambuco, Recife, Brazil
| | - André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Arapiraca, Brazil.,Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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