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Li QQ, Zhang ZP, Aogan, Wen J. Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications. FRONTIERS IN PLANT SCIENCE 2024; 15:1349358. [PMID: 38766467 PMCID: PMC11099909 DOI: 10.3389/fpls.2024.1349358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/25/2024] [Indexed: 05/22/2024]
Abstract
The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.
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Affiliation(s)
- Qin-Qin Li
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
- Key Laboratory of Biodiversity Conservation and Sustainable Utilization in Mongolian Plateau for College and University of Inner Mongolia Autonomous Region, Hohhot, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Ping Zhang
- College of Computer Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Aogan
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
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Laczkó L, Jordán S, Póliska S, Rácz HV, Nagy NA, Molnár V A, Sramkó G. The draft genome of Spiraea crenata L. (Rosaceae) - the first complete genome in tribe Spiraeeae. Sci Data 2024; 11:219. [PMID: 38368431 PMCID: PMC10874383 DOI: 10.1038/s41597-024-03046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome in tribe Spiraeeae, this may not only be the first step in the genomic study of a rare plant but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of Rosaceae.
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Affiliation(s)
- Levente Laczkó
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary
| | - Sándor Jordán
- Department of Metagenomics, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary
- Juhász-Nagy Pál Doctoral School, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Hanna Viktória Rácz
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Nikoletta Andrea Nagy
- Department of Evolutionary Zoology and Human Biology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
- HUN-REN-UD Behavioural Ecology Research Group, University of Debrecen, Debrecen, Hungary
| | - Attila Molnár V
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary
- Evolutionary Genomics Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Gábor Sramkó
- HUN-REN-UD Conservation Biology Research Group, University of Debrecen, Debrecen, Hungary.
- Evolutionary Genomics Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary.
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Zhang SY, Yan HF, Wei L, Liu TJ, Chen L, Hao G, Wu X, Zhang QL. Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae). BMC PLANT BIOLOGY 2024; 24:23. [PMID: 38166728 PMCID: PMC10763413 DOI: 10.1186/s12870-023-04697-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. RESULTS In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113-114 genes, including 78-79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30 Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. CONCLUSIONS The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus.
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Affiliation(s)
- Shu-Yan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lei Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tong-Jian Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Lin Chen
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Qiao-Ling Zhang
- Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou, 310013, China.
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