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Corvalán LCJ, Sobreiro MB, Carvalho LR, Dias RO, Braga-Ferreira RS, Targueta CP, Silva-Neto CME, Berton BW, Pereira AMS, Diniz-filho JAF, Telles MPC, Nunes R. Chloroplast genome assembly of Serjania erecta Raldk: comparative analysis reveals gene number variation and selection in protein-coding plastid genes of Sapindaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1258794. [PMID: 37822334 PMCID: PMC10562606 DOI: 10.3389/fpls.2023.1258794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023]
Abstract
Serjania erecta Raldk is an essential genetic resource due to its anti-inflammatory, gastric protection, and anti-Alzheimer properties. However, the genetic and evolutionary aspects of the species remain poorly known. Here, we sequenced and assembled the complete chloroplast genome of S. erecta and used it in a comparative analysis within the Sapindaceae family. S. erecta has a chloroplast genome (cpDNA) of 159,297 bp, divided into a Large Single Copy region (LSC) of 84,556 bp and a Small Single Copy region (SSC) of 18,057 bp that are surrounded by two Inverted Repeat regions (IRa and IRb) of 28,342 bp. Among the 12 species used in the comparative analysis, S. erecta has the fewest long and microsatellite repeats. The genome structure of Sapindaceae species is relatively conserved; the number of genes varies from 128 to 132 genes, and this variation is associated with three main factors: (1) Expansion and retraction events in the size of the IRs, resulting in variations in the number of rpl22, rps19, and rps3 genes; (2) Pseudogenization of the rps2 gene; and (3) Loss or duplication of genes encoding tRNAs, associated with the duplication of trnH-GUG in X. sorbifolium and the absence of trnT-CGU in the Dodonaeoideae subfamily. We identified 10 and 11 mutational hotspots for Sapindaceae and Sapindoideae, respectively, and identified six highly diverse regions (tRNA-Lys - rps16, ndhC - tRNA-Val, petA - psbJ, ndhF, rpl32 - ccsA, and ycf1) are found in both groups, which show potential for the development of DNA barcode markers for molecular taxonomic identification of Serjania. We identified that the psaI gene evolves under neutrality in Sapindaceae, while all other chloroplast genes are under strong negative selection. However, local positive selection exists in the ndhF, rpoC2, ycf1, and ycf2 genes. The genes ndhF and ycf1 also present high nucleotide diversity and local positive selection, demonstrating significant potential as markers. Our findings include providing the first chloroplast genome of a member of the Paullinieae tribe. Furthermore, we identified patterns in variations in the number of genes and selection in genes possibly associated with the family's evolutionary history.
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Affiliation(s)
| | - Mariane B. Sobreiro
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Larissa R. Carvalho
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Renata O. Dias
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | - Ramilla S. Braga-Ferreira
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto de Ciências Exatas e Naturais, Universidade Federal de Rondonópolis, Rondonópolis, Brazil
| | - Cintia P. Targueta
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
| | | | | | | | - José A. F. Diniz-filho
- Laboratório de Ecologia Teórica e Síntese, Universidade Federal de Goiás, Goiânia, Brazil
| | - Mariana P. C. Telles
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Brazil
| | - Rhewter Nunes
- Laboratório de Genética & Biodiversidade, Universidade Federal de Goiás, Goiânia, Brazil
- Instituto Federal de Goiás, Goiás, Brazil
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Cunha Neto IL. Vascular variants in seed plants-a developmental perspective. AOB PLANTS 2023; 15:plad036. [PMID: 37476579 PMCID: PMC10355320 DOI: 10.1093/aobpla/plad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/04/2023] [Indexed: 07/22/2023]
Abstract
Over centuries of plant morphological research, biologists have enthusiastically explored how distinct vascular arrangements have diversified. These investigations have focused on the evolution of steles and secondary growth and examined the diversity of vascular tissues (xylem and phloem), including atypical developmental pathways generated through modifications to the typical development of ancestral ontogenies. A shared vernacular has evolved for communicating on the diversity of alternative ontogenies in seed plants. Botanists have traditionally used the term 'anomalous secondary growth' which was later renamed to 'cambial variants' by late Dr. Sherwin Carlquist (1988). However, the term 'cambial variants' can be vague in meaning since it is applied for developmental pathways that do not necessarily originate from cambial activity. Here, we review the 'cambial variants' concept and propose the term 'vascular variants' as a more inclusive overarching framework to interpret alternative vascular ontogenies in plants. In this framework, vascular variants are defined by their developmental origin (instead of anatomical patterns), allowing the classification of alternative vascular ontogenies into three categories: (i) procambial variants, (ii) cambial variants and (iii) ectopic cambia. Each category includes several anatomical patterns. Vascular variants, which represent broader developmental based groups, can be applied to both extant and fossil plants, and thereby offer a more adequate term from an evolutionary perspective. An overview of the developmental diversity and phylogenetic distribution of vascular variants across selected seed plants is provided. Finally, this viewpoint discusses the evolutionary implications of vascular variants.
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Wilf P, Wing SL, Meyer HW, Rose JA, Saha R, Serre T, Cúneo NR, Donovan MP, Erwin DM, Gandolfo MA, González-Akre E, Herrera F, Hu S, Iglesias A, Johnson KR, Karim TS, Zou X. An image dataset of cleared, x-rayed, and fossil leaves vetted to plant family for human and machine learning. PHYTOKEYS 2021; 187:93-128. [PMID: 35068970 PMCID: PMC8702526 DOI: 10.3897/phytokeys.187.72350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/05/2021] [Indexed: 05/04/2023]
Abstract
Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.
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Affiliation(s)
- Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USAPennsylvania State UniversityUniversity ParkUnited States of America
| | - Scott L. Wing
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USADepartment of Paleobiology, Smithsonian InstitutionWashington, DCUnited States of America
| | - Herbert W. Meyer
- Florissant Fossil Beds National Monument, National Park Service, Florissant, CO 80816, USAFlorissant Fossil Beds National Monument, National Park ServiceFlorissantUnited States of America
| | - Jacob A. Rose
- School of Engineering, Brown University, Providence, RI 02912, USABrown UniversityProvidenceUnited States of America
| | - Rohit Saha
- Department of Cognitive, Linguistic and Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USAMuseo Paleontológico E. FeruglioTrelewArgentina
| | - Thomas Serre
- Department of Cognitive, Linguistic and Psychological Sciences, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USAMuseo Paleontológico E. FeruglioTrelewArgentina
| | - N. Rubén Cúneo
- CONICET-Museo Paleontológico Egidio Feruglio, Trelew 9100, Chubut, Argentinaepartment of Paleobotany and Paleoecology, Cleveland Museum of Natural HistoryClevelandUnited States of America
| | - Michael P. Donovan
- Department of Paleobotany and Paleoecology, Cleveland Museum of Natural History, Cleveland, OH 44106, USAUniversity of California-BerkeleyBerkeleyUnited States of America
| | - Diane M. Erwin
- University of California-Berkeley, Museum of Paleontology, Berkeley, CA 94720, USACornell UniversityIthacaUnited States of America
| | - María A. Gandolfo
- LH Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USASmithsonian Conservation Biology Institute, National Zoological Park,Front RoyalUnited States of America
| | - Erika González-Akre
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, 22630, USANegaunee Integrative Research Center, Field Museum of Natural HistoryChicagoUnited States of America
| | - Fabiany Herrera
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USAYale UniversityNew HavenUnited States of America
| | - Shusheng Hu
- Division of Paleobotany, Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USAInstituto de Investigaciones en Biodiversidad y Ambiente INIBIOMA, CONICET-UNComaSan Carlos de BarilocheArgentina
| | - Ari Iglesias
- Instituto de Investigaciones en Biodiversidad y Ambiente INIBIOMA, CONICET-UNComa, San Carlos de Bariloche 8400, Río Negro, ArgentinaDepartment of Paleobiology, Smithsonian InstitutionWashingtonUnited States of America
| | - Kirk R. Johnson
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USADepartment of Paleobiology, Smithsonian InstitutionWashington, DCUnited States of America
| | - Talia S. Karim
- University of Colorado Museum of Natural History, Boulder, CO 80503, USAUniversity of Colorado Museum of Natural HistoryBoulderUnited States of America
| | - Xiaoyu Zou
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, PA 16802, USAPennsylvania State UniversityUniversity ParkUnited States of America
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