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Chen Q, Hu H, Zhang D. DNA Barcoding and Phylogenomic Analysis of the Genus Fritillaria in China Based on Complete Chloroplast Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:764255. [PMID: 35283910 PMCID: PMC8914171 DOI: 10.3389/fpls.2022.764255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/21/2022] [Indexed: 05/10/2023]
Abstract
The Fritillaria is an extremely complicated genus in taxonomy and phylogeny, which contains numerous medicinal species in China. Both traditional characteristic-based taxonomy and universal DNA barcodes (ITS, trnH-psbA, and rbcL) are difficult to effectively identify the species. Here, we generated a large dataset of chloroplast genomes from multiple accessions per species of Fritillaria to evaluate their effectiveness in species discrimination. Moreover, phylogeny of species in China was explored based on the complete chloroplast genomes, and then divergence times of each node were estimated. The results showed that all 21 species in Fritillaria here (including two suspicious species) could be correctly discriminated using cpDNA genomes except F. cirrhosa, which suggested that DNA super-barcode could greatly enhance species discriminatory resolution for complicated genera. Furthermore, four regions (ycf1, matK-trnG-GCC, rpoC1, and matK) gained remarkably higher resolution than that of other plastid regions, but only matK might be suitable to identify Fritillaria species in consideration of its lengths. Phylogenomic analysis showed that the subgenus Fritillaria in China was divided into four major clades with obvious geographic structure. Among them, Clade I, mainly distributed in southwest China, was a young and complicated group. Moreover, according to the analysis, taxonomic treatments of the two suspicious species, namely "F. omeiensis" and "F. hupehensis" in Flora of China (2000) are questionable and might need further revision. Molecular dating revealed that both origin and divergence of subgenus Fritillaria, as well as its four major clades, were significantly associated with geological and climatic fluctuations during the Middle to Late Miocene. This study would enrich case studies of DNA super-barcode and provide new insights on speciation, lineage diversification, and biogeography of the Fritillaria in China.
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Affiliation(s)
- Qi Chen
- College of Pharmacy, Dali University, Dali, China
| | - Haisu Hu
- College of Pharmacy, Dali University, Dali, China
| | - Dequan Zhang
- College of Pharmacy, Dali University, Dali, China
- Institute of Materia Medica, Dali University, Dali, China
- *Correspondence: Dequan Zhang,
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202
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Wang J, Fu CN, Mo ZQ, Möller M, Yang JB, Zhang ZR, Li DZ, Gao LM. Testing the Complete Plastome for Species Discrimination, Cryptic Species Discovery and Phylogenetic Resolution in Cephalotaxus (Cephalotaxaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:768810. [PMID: 35599857 PMCID: PMC9116380 DOI: 10.3389/fpls.2022.768810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/07/2022] [Indexed: 05/17/2023]
Abstract
Species of Cephalotaxus have great economic and ecological values. However, the taxonomy and interspecific phylogenetic relationships within the genus have been controversial and remained not fully resolved until now. To date, no study examined the efficiency of the complete plastome as super-barcode across Cephalotaxus species with multiple samples per taxon. In this study, we have evaluated the complete plastome in species discrimination and phylogenetic resolution in Cephalotaxus by including 32 individuals of all eight recognized species and five varieties following Farjon's classification (2010) with multiple samples per taxon. Our results indicated that not all species recognized in recent taxonomic revisions of Cephalotaxus could be distinguished and not all were monophyletic. Based on the plastome phylogeny, a new taxonomic classification for the genus comprising nine species and two varieties, including a cryptic species, was proposed. The phylogeny also resolved all interspecific relationships. Compared to the plastome based classification, standard DNA barcodes, alone or in combination, only recognized a maximum of seven out of the nine species. Moreover, two highly variable single loci, ycf1 and rps16, each alone achieved full species discrimination. With the moderate length of 1079 bp, rps16 is proposed as a specific barcode to discriminate Cephalotaxus species. The super-barcodes and specific barcode candidates will aid in the identification of endangered Cephalotaxus species, and to help focus conservation measures.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
- *Correspondence: Lian-Ming Gao,
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203
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Maurin KJL, Smissen RD, Lusk CH. A dated phylogeny shows Plio-Pleistocene climates spurred evolution of antibrowsing defences in the New Zealand flora. THE NEW PHYTOLOGIST 2022; 233:546-554. [PMID: 34610149 PMCID: PMC9298021 DOI: 10.1111/nph.17766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Some plant traits may be legacies of coevolution with extinct megafauna. One example is the convergent evolution of 'divaricate' cage architectures in many New Zealand lineages, interpreted as a response to recently extinct flightless avian browsers whose ancestors arrived during the Paleogene period. Although experiments have confirmed that divaricate habit deters extant browsers, its abundance on frosty, droughty sites appears consistent with an earlier interpretation as a response to cold, dry Plio-Pleistocene climates. We used 45 protein-coding sequences from plastid genomes to reconstruct the evolutionary history of the divaricate habit in extant New Zealand lineages. Our dated phylogeny of 215 species included 91% of New Zealand eudicot divaricate species. We show that 86% of extant divaricate plants diverged from non-divaricate sisters within the last 5 Ma, implicating Plio-Pleistocene climates in the proliferation of cage architectures in New Zealand. Our results, combined with other recent findings, are consistent with the synthetic hypothesis that the browser-deterrent effect of cage architectures was strongly selected only when Plio-Pleistocene climatic constraints prevented woody plants from growing quickly out of reach of browsers. This is consistent with the abundance of cage architectures in other regions where plant growth is restricted by aridity or short frost-free periods.
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Affiliation(s)
| | - Rob D. Smissen
- Allan HerbariumManaaki Whenua – Landcare ResearchLincoln7640New Zealand
| | - Christopher H. Lusk
- Environmental Research InstituteThe University of WaikatoHamilton3240New Zealand
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204
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Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 233:329-343. [PMID: 34637542 DOI: 10.1111/nph.17792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development.
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Affiliation(s)
- Ivan Kashkan
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Mónika Hrtyan
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 166 10, Czech Republic
| | - Aswathy Jayasree
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Roberta Filepová
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Zuzana Vondráková
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Sibu Simon
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Debbie Rombaut
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland
| | - Jan Hejátko
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
| | - Jiří Friml
- Institute of Science and Technology (IST Austria), Klosterneuburg, 3400, Austria
| | - Jan Petrášek
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
| | - Kamil Růžička
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, 16502, Czech Republic
- Functional Genomics and Proteomics of Plants, Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University, Brno, 62500, Czech Republic
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205
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Woudstra Y, Viruel J, Fritzsche M, Bleazard T, Mate R, Howard C, Rønsted N, Grace OM. A customised target capture sequencing tool for molecular identification of Aloe vera and relatives. Sci Rep 2021; 11:24347. [PMID: 34934068 PMCID: PMC8692607 DOI: 10.1038/s41598-021-03300-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.
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Affiliation(s)
- Yannick Woudstra
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK.
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark.
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Surrey, TW9 3AE, UK
| | - Martin Fritzsche
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Thomas Bleazard
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Ryan Mate
- National Institute of Biological Standards and Control, South Mimms, UK
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Saffron Walden, CB10 1RQ, UK
| | - Nina Rønsted
- Natural History Museum Denmark, University of Copenhagen, Gothersgade 130, 1153, Copenhagen, Denmark
- National Tropical Botanical Garden, 3530 Papalina Road, Kalaheo, HI, 96741, USA
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206
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Tominaga T, Miura C, Sumigawa Y, Hirose Y, Yamaguchi K, Shigenobu S, Mine A, Kaminaka H. Conservation and Diversity in Gibberellin-Mediated Transcriptional Responses Among Host Plants Forming Distinct Arbuscular Mycorrhizal Morphotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:795695. [PMID: 34975984 PMCID: PMC8718060 DOI: 10.3389/fpls.2021.795695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/12/2021] [Indexed: 06/01/2023]
Abstract
Morphotypes of arbuscular mycorrhizal (AM) symbiosis, Arum, Paris, and Intermediate types, are mainly determined by host plant lineages. It was reported that the phytohormone gibberellin (GA) inhibits the establishment of Arum-type AM symbiosis in legume plants. In contrast, we previously reported that GA promotes the establishment of Paris-type AM symbiosis in Eustoma grandiflorum, while suppressing Arum-type AM symbiosis in a legume model plant, Lotus japonicus. This raises a hitherto unexplored possibility that GA-mediated transcriptional reprogramming during AM symbiosis is different among plant lineages as the AM morphotypes are distinct. Here, our comparative transcriptomics revealed that several symbiosis-related genes were commonly upregulated upon AM fungal colonization in L. japonicus (Arum-type), Daucus carota (Intermediate-type), and E. grandiflorum (Paris-type). Despite of the similarities, the fungal colonization levels and the expression of symbiosis-related genes were suppressed in L. japonicus and D. carota but were promoted in E. grandiflorum in the presence of GA. Moreover, exogenous GA inhibited the expression of genes involved in biosynthetic process of the pre-symbiotic signal component, strigolactone, which resulted in the reduction of its endogenous accumulation in L. japonicus and E. grandiflorum. Additionally, differential regulation of genes involved in sugar metabolism suggested that disaccharides metabolized in AM roots would be different between L. japonicus and D. carota/E. grandiflorum. Therefore, this study uncovered the conserved transcriptional responses during mycorrhization regardless of the distinct AM morphotype. Meanwhile, we also found diverse responses to GA among phylogenetically distant AM host plants.
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Affiliation(s)
- Takaya Tominaga
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Chihiro Miura
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Yuuka Sumigawa
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Yukine Hirose
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Akira Mine
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- JST, PRESTO, Kawaguchi, Japan
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207
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Zhang Y, Song MF, Li Y, Sun HF, Tang DY, Xu AS, Yin CY, Zhang ZL, Zhang LX. Complete Chloroplast Genome Analysis of Two Important Medicinal Alpinia Species: Alpinia galanga and Alpinia kwangsiensis. FRONTIERS IN PLANT SCIENCE 2021; 12:705892. [PMID: 34975932 PMCID: PMC8714959 DOI: 10.3389/fpls.2021.705892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/18/2021] [Indexed: 06/03/2023]
Abstract
Most Alpinia species are valued as foods, ornamental plants, or plants with medicinal properties. However, morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Alpinia species. Difficulties in species identification have led to confusion in the sale and use of Alpinia for medicinal use. To mine resources and improve the molecular methods for distinguishing among Alpinia species, we report the complete chloroplast (CP) genomes of Alpinia galanga and Alpinia kwangsiensis species, obtained via high-throughput Illumina sequencing. The CP genomes of A. galanga and A. kwangsiensis exhibited a typical circular tetramerous structure, including a large single-copy region (87,565 and 87,732 bp, respectively), a small single-copy region (17,909 and 15,181 bp, respectively), and a pair of inverted repeats (27,313 and 29,705 bp, respectively). The guanine-cytosine content of the CP genomes is 36.26 and 36.15%, respectively. Furthermore, each CP genome contained 133 genes, including 87 protein-coding genes, 38 distinct tRNA genes, and 8 distinct rRNA genes. We identified 110 and 125 simple sequence repeats in the CP genomes of A. galanga and A. kwangsiensis, respectively. We then combined these data with publicly available CP genome data from four other Alpinia species (A. hainanensis, A. oxyphylla, A. pumila, and A. zerumbet) and analyzed their sequence characteristics. Nucleotide diversity was analyzed based on the alignment of the complete CP genome sequences, and five candidate highly variable site markers (trnS-trnG, trnC-petN, rpl32-trnL, psaC-ndhE, and ndhC-trnV) were found. Twenty-eight complete CP genome sequences belonging to Alpinieae species were used to construct phylogenetic trees. The results fully demonstrated the phylogenetic relationship among the genera of the Alpinieae, and further proved that Alpinia is a non-monophyletic group. The complete CP genomes of the two medicinal Alpinia species provides lays the foundation for the use of CP genomes in species identification and phylogenetic analyses of Alpinia species.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhong-Lian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
| | - Li-Xia Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Jinghong, China
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208
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Yu T, Hu Y, Zhang Y, Zhao R, Yan X, Dayananda B, Wang J, Jiao Y, Li J, Yi X. Whole-Genome Sequencing of Acer catalpifolium Reveals Evolutionary History of Endangered Species. Genome Biol Evol 2021; 13:6456308. [PMID: 34878129 PMCID: PMC8677443 DOI: 10.1093/gbe/evab271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 01/27/2023] Open
Abstract
Acer catalpifolium is an endangered species restricted to remote localities of West China. Understanding the genomic content and evolution of A. catalpifolium is essential to conservation efforts of this rare and ecologically valuable plant. Here, we report a high-quality genome of A. catalpifolium consisting of ∼654 Mbp and ∼35,132 protein-coding genes. We detected 969 positively selected genes in two Acer genomes compared with four other eudicots, 65 of which were transcription factors. We hypothesize that these positively selected mutations in transcription factors might affect their function and thus contribute to A. catalpifolium’s decline-type population. We also identified 179 significantly expanded gene families compared with 12 other eudicots, some of which are involved in stress responses, such as the FRS–FRF family. We inferred that A. catalpifolium has experienced gene family expansions to cope with environmental stress in its evolutionary history. Finally, 109 candidate genes encoding key enzymes in the lignin biosynthesis pathway were identified in A. catalpifolium; of particular note were the large range and high copy number of cinnamyl alcohol dehydrogenase genes. The chromosome-level genome of A. catalpifolium presented here may serve as a fundamental genomic resource for better understanding endangered Acer species, informing future conservation efforts.
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Affiliation(s)
- Tao Yu
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuyang Zhang
- The National-Local Joint Engineering Laboratory of High Efficiency and Superior-Quality Cultivation and Fruit Deep Processing Technology on Characteristic Fruit Trees, College of Plant Science, Tarim University, Alear, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Buddhi Dayananda
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junqing Li
- Beijing Key Laboratory for Forest Resources and Ecosystem Processes, Beijing Forestry University, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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209
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Åstrand J, Knight C, Robson J, Talle B, Wilson ZA. Evolution and diversity of the angiosperm anther: trends in function and development. PLANT REPRODUCTION 2021; 34:307-319. [PMID: 34173886 PMCID: PMC8566645 DOI: 10.1007/s00497-021-00416-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/28/2021] [Indexed: 05/21/2023]
Abstract
Anther development and dehiscence is considered from an evolutionary perspective to identify drivers for differentiation, functional conservation and to identify key questions for future male reproduction research. Development of viable pollen and its timely release from the anther are essential for fertilisation of angiosperm flowers. The formation and subsequent dehiscence of the anther are under tight regulatory control, and these processes are remarkably conserved throughout the diverse families of the angiosperm clade. Anther development is a complex process, which requires timely formation and communication between the multiple somatic anther cell layers (the epidermis, endothecium, middle layer and tapetum) and the developing pollen. These layers go through regulated development and selective degeneration to facilitate the formation and ultimate release of the pollen grains. Insight into the evolution and divergence of anther development and dehiscence, especially between monocots and dicots, is driving greater understanding of the male reproductive process and increased, resilient crop yields. This review focuses on anther structure from an evolutionary perspective by highlighting their diversity across plant species. We summarise new findings that illustrate the complexities of anther development and evaluate how they challenge established models of anther form and function, and how they may help to deliver future sustainable crop yields.
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Affiliation(s)
- Johanna Åstrand
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Christopher Knight
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Jordan Robson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Behzad Talle
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Zoe A. Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
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210
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Wei R, Yang J, He LJ, Liu HM, Hu JY, Liang SQ, Wei XP, Zhao CF, Zhang XC. Plastid phylogenomics provides novel insights into the infrafamilial relationship of Polypodiaceae. Cladistics 2021; 37:717-727. [PMID: 34841589 DOI: 10.1111/cla.12461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 01/01/2023] Open
Abstract
The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Juan He
- Xiamen Overseas Chinese Subtropical Plant Introduction Garden/Plant Introduction & Quarantine and Plant Product Key Laboratory of Xiamen, Xiamen, Fujian, 361002, China
| | - Hong-Mei Liu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Jia-Yu Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Si-Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue-Ping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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211
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Lemnaceae and Orontiaceae Are Phylogenetically and Morphologically Distinct from Araceae. PLANTS 2021; 10:plants10122639. [PMID: 34961110 PMCID: PMC8704351 DOI: 10.3390/plants10122639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/18/2022]
Abstract
Duckweeds comprise a distinctive clade of pleustophytic monocots that traditionally has been classified as the family Lemnaceae. However, molecular evidence has called into question their phylogenetic independence, with some authors asserting instead that duckweeds should be reclassified as subfamily Lemnoideae of an expanded family Araceae. Although a close phylogenetic relationship of duckweeds with traditional Araceae has been supported by multiple studies, the taxonomic disposition of duckweeds must be evaluated more critically to promote nomenclatural stability and utility. Subsuming duckweeds as a morphologically incongruent lineage of Araceae effectively eliminates the family category of Lemnaceae that has been widely used for many years. Instead, we suggest that Araceae subfamily Orontioideae should be restored to family status as Orontiaceae, which thereby would enable the recognition of three morphologically and phylogenetically distinct lineages: Araceae, Lemnaceae, and Orontiaceae.
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212
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Guo X, Fang D, Sahu SK, Yang S, Guang X, Folk R, Smith SA, Chanderbali AS, Chen S, Liu M, Yang T, Zhang S, Liu X, Xu X, Soltis PS, Soltis DE, Liu H. Chloranthus genome provides insights into the early diversification of angiosperms. Nat Commun 2021; 12:6930. [PMID: 34836973 PMCID: PMC8626473 DOI: 10.1038/s41467-021-26922-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.
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Affiliation(s)
- Xing Guo
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Dongming Fang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Sunil Kumar Sahu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shuai Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Xuanmin Guang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ryan Folk
- grid.260120.70000 0001 0816 8287Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762 United States of America
| | - Stephen A. Smith
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 United States of America
| | - Andre S. Chanderbali
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Sisi Chen
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.9227.e0000000119573309South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650 China
| | - Min Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Ting Yang
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China
| | - Shouzhou Zhang
- grid.9227.e0000000119573309Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen, Chinese Academy of Sciences, Shenzhen, 518004 China
| | - Xin Liu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839BGI-Fuyang, BGI-Shenzhen, Fuyang, 236009 China
| | - Xun Xu
- grid.21155.320000 0001 2034 1839State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083 China ,grid.21155.320000 0001 2034 1839Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518083 China
| | - Pamela S. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America
| | - Douglas E. Soltis
- grid.15276.370000 0004 1936 8091Florida Museum of Natural History, University of Florida, Gainesville, FL United States of America ,grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, FL 32611 United States of America
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark.
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213
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Ma J, Sun P, Wang D, Wang Z, Yang J, Li Y, Mu W, Xu R, Wu Y, Dong C, Shrestha N, Liu J, Yang Y. The Chloranthus sessilifolius genome provides insight into early diversification of angiosperms. Nat Commun 2021; 12:6929. [PMID: 34836967 PMCID: PMC8626421 DOI: 10.1038/s41467-021-26931-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Most extant angiosperms belong to Mesangiospermae, which comprises eudicots, monocots, magnoliids, Chloranthales and Ceratophyllales. However, phylogenetic relationships between these five lineages remain unclear. Here, we report the high-quality genome of a member of the Chloranthales lineage (Chloranthus sessilifolius). We detect only one whole genome duplication within this species and find that polyploidization events in different Mesangiospermae lineage are mutually independent. We also find that the members of all floral development-related gene lineages are present in C. sessilifolius despite its extremely simplified flower. The AP1 and PI genes, however, show a weak floral tissue-specialized expression. Our phylogenomic analyses suggest that Chloranthales and magnoliids are sister groups, and both are together sister to the clade comprising Ceratophyllales and eudicots, while the monocot lineage is sister to all other Mesangiospermae. Our findings suggest that in addition to hybridization, incomplete lineage sorting may largely account for phylogenetic inconsistencies between the observed gene trees.
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Affiliation(s)
- Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Dandan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhenyue Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jiao Yang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Congcong Dong
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China.
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214
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Heringer P, Kuhn GCS. Pif1 helicases and the evidence for a prokaryotic origin of Helitrons. Mol Biol Evol 2021; 39:6440065. [PMID: 34850089 PMCID: PMC8788227 DOI: 10.1093/molbev/msab334] [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] [Indexed: 12/31/2022] Open
Abstract
Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and nonmetric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.
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Affiliation(s)
- Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP, 31270-901, Brazil
| | - Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, CEP, 31270-901, Brazil
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215
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Luo Y, He J, Lyu R, Xiao J, Li W, Yao M, Pei L, Cheng J, Li J, Xie L. Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae. Front Genet 2021; 12:730495. [PMID: 34804117 PMCID: PMC8600051 DOI: 10.3389/fgene.2021.730495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/20/2021] [Indexed: 02/01/2023] Open
Abstract
The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.
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Affiliation(s)
- Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jiamin Xiao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wenhe Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinyu Li
- Beijing Institute of Landscape Architecture, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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216
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Song T, Zhou M, Yuan Y, Yu J, Cai H, Li J, Chen Y, Bai Y, Zhou G, Cui G. Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern. FRONTIERS IN PLANT SCIENCE 2021; 12:770660. [PMID: 34868169 PMCID: PMC8637744 DOI: 10.3389/fpls.2021.770660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Amphicarpaea edgeworthii, an annual twining herb, is a widely distributed species and an attractive model for studying complex flowering types and evolutionary mechanisms of species. Herein, we have generated a high-quality assembly of A. edgeworthii by using a combination of PacBio, 10× Genomics libraries, and Hi-C mapping technologies. The final 11 chromosome-level scaffolds covered 90.61% of the estimated genome (343.78Mb), which is a chromosome-scale assembled genome of an amphicarpic plant. Subsequently, we characterized the genetic diversity and population structure of A. edgeworthii species by resequencing individuals collected from their natural area of distribution. Using transcriptome profiling, we observed that specific phenotypes are regulated by a complex network of light, hormones, and MADS-box gene families. These data are beneficial for the discovery of genes that control major agronomic traits and spur genetic improvement of and functional genetic studies in legumes, as well as supply comparative genetic resources for other amphicarpic plants.
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Affiliation(s)
- Tingting Song
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuying Yuan
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jinqiu Yu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hua Cai
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yan Bai
- Novogene Bioinformatics Institute, Beijing, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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217
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Walker M, Pérez M, Steinbrecher T, Gawthrop F, Pavlović I, Novák O, Tarkowská D, Strnad M, Marone F, Nakabayashi K, Leubner-Metzger G. Molecular mechanisms and hormonal regulation underpinning morphological dormancy: a case study using Apium graveolens (Apiaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1020-1036. [PMID: 34510583 DOI: 10.1111/tpj.15489] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Underdeveloped (small) embryos embedded in abundant endosperm tissue, and thus having morphological dormancy (MD) or morphophysiological dormancy (MPD), are considered to be the ancestral state in seed dormancy evolution. This trait is retained in the Apiaceae family, which provides excellent model systems for investigating the underpinning mechanisms. We investigated Apium graveolens (celery) MD by combined innovative imaging and embryo growth assays with the quantification of hormone metabolism, as well as the analysis of hormone and cell-wall related gene expression. The integrated experimental results demonstrated that embryo growth occurred inside imbibed celery fruits in association with endosperm degradation, and that a critical embryo size was required for radicle emergence. The regulation of these processes depends on gene expression leading to gibberellin and indole-3-acetic acid (IAA) production by the embryo and on crosstalk between the fruit compartments. ABA degradation associated with distinct spatiotemporal patterns in ABA sensitivity control embryo growth, endosperm breakdown and radicle emergence. This complex interaction between gibberellins, IAA and ABA metabolism, and changes in the tissue-specific sensitivities to these hormones is distinct from non-MD seeds. We conclude that the embryo growth to reach the critical size and the associated endosperm breakdown inside MD fruits constitute a unique germination programme.
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Affiliation(s)
- Matthew Walker
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
- Tozer Seeds, Tozer Seeds Ltd, Cobham, KT11 3EH, UK
| | - Marta Pérez
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Tina Steinbrecher
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | | | - Iva Pavlović
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371, Czech Republic
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371, Czech Republic
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen, CH-5232, Switzerland
| | - Kazumi Nakabayashi
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Gerhard Leubner-Metzger
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Faculty of Science, Palacký University Olomouc, Olomouc, CZ-78371, Czech Republic
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218
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Davis SN, Clarke JA. Estimating the distribution of carotenoid coloration in skin and integumentary structures of birds and extinct dinosaurs. Evolution 2021; 76:42-57. [PMID: 34719783 DOI: 10.1111/evo.14393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/27/2022]
Abstract
Carotenoids are pigments responsible for most bright yellow, red, and orange hues in birds. Their distribution has been investigated in avian plumage, but the evolution of their expression in skin and other integumentary structures has not been approached in detail. Here, we investigate the expression of carotenoid-consistent coloration across tissue types in all extant, nonpasserine species (n = 4022) and archelosaur outgroups in a phylogenetic framework. We collect dietary data for a subset of birds and investigate how dietary carotenoid intake may relate to carotenoid expression in various tissues. We find that carotenoid-consistent expression in skin or nonplumage keratin has a 50% probability of being present in the most recent common ancestor of Archosauria. Skin expression has a similar probability at the base of the avian crown clade, but plumage expression is unambiguously absent in that ancestor and shows hundreds of independent gains within nonpasserine neognaths, consistent with previous studies. Although our data do not support a strict sequence of tissue expression in nonpasserine birds, we find support that expression of carotenoid-consistent color in nonplumage integument structures might evolve in a correlated manner and feathers are rarely the only region of expression. Taxa with diets high in carotenoid content also show expression in more body regions and tissue types. Our results may inform targeted assays for carotenoids in tissues other than feathers, and expectations of these pigments in nonavian dinosaurs. In extinct groups, bare-skin regions and the rhamphotheca, especially in species with diets rich in plants, may express these pigments, which are not expected in feathers or feather homologues.
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Affiliation(s)
- Sarah N Davis
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712
| | - Julia A Clarke
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, 78712.,Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712
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219
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Li HT, Luo Y, Gan L, Ma PF, Gao LM, Yang JB, Cai J, Gitzendanner MA, Fritsch PW, Zhang T, Jin JJ, Zeng CX, Wang H, Yu WB, Zhang R, van der Bank M, Olmstead RG, Hollingsworth PM, Chase MW, Soltis DE, Soltis PS, Yi TS, Li DZ. Plastid phylogenomic insights into relationships of all flowering plant families. BMC Biol 2021; 19:232. [PMID: 34711223 PMCID: PMC8555322 DOI: 10.1186/s12915-021-01166-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades. RESULTS Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation. CONCLUSIONS We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.
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Affiliation(s)
- Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lu Gan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Ecosystem National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jie Cai
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Matthew A Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76017, USA
| | - Ting Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10025, USA
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hong Wang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Michelle van der Bank
- Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195-5325, USA
| | | | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, England, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Li ZZ, Lehtonen S, Martins K, Wang QF, Chen JM. Complete genus-level plastid phylogenomics of Alismataceae with revisited historical biogeography. Mol Phylogenet Evol 2021; 166:107334. [PMID: 34715331 DOI: 10.1016/j.ympev.2021.107334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022]
Abstract
Alismataceae, an ancient lineage of monocots, has attracted attention due to its complex evolutionary history, ornamental value, and ecological role. However, the phylogenetic relationships and evolutionary history of the family have not been conclusively resolved. Here, we constructed the first complete genus-level plastid phylogeny of Alismataceae by using 78 genes and updated the historical biogeography based on the phylogenomic tree. Our results divide the Alismataceae into three major clades with robust support values; one clade comprises the former Limnocharitaceae, and the second clade includes the mainly temperate genera Alisma, Baldellia, Damasonium and Luronium, and the monotypic African genus Burnatia as a sister of the temperate genera. The remaining genera are either tropical or have some temperate species in addition to tropical ones, and they constitute the third major clade. Molecular dating and biogeographic analyses suggest that Alismataceae arose in Neotropical, West Palearctic, and Afrotropical regions during the Cretaceous, followed by the split into three main clades due to a combination of vicariance and dispersal events. Unlike earlier studies, we inferred that the mainly temperate clade likely originated from Afrotropical and West Palearctic regions during the Eocene. The most recent common ancestor of the other two clades lived in the Neotropical area during the Late Cretaceous. Long-distance dispersal and vicariance together seem to contribute to the transoceanic distribution of this family.
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Affiliation(s)
- Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Samuli Lehtonen
- Herbarium, Biodiversity Unit, University of Turku, Turku 20014, Finland
| | - Karina Martins
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba 18052-780, Brazil
| | - Qing-Feng Wang
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Jin-Ming Chen
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China.
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221
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Li L, Liu GM, Zhang ZR, Corlett RT, Yu WB. Characteristics of the complete chloroplast genome sequences of Stylidium debile and Stylidium petiolare (Stylidiaceae). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:3134-3136. [PMID: 34660891 PMCID: PMC8519543 DOI: 10.1080/23802359.2021.1985403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We report complete chloroplast genome (plastome) sequences of Stylidium debile (150,105 bp) and Stylidium petiolare (150,998 bp). Both plastomes had the typical quadripartite structure, with large single-copy (LSC) and small single-copy (SSC) regions separated by two inverted repeat (IR) regions. Both plastomes have lost the rps19 and ycf15 CDS genes, and had infA-like, rps22-like, and rps7-like pseudogenes. Moreover, IR regions were expanded by having trnH GUG tRNA and the rps22-like pseudogene. Plastome phylogenomic analyses showed that the two Stylidium species formed a monophyletic clade (BS = 100), sister to the Argophyllaceae (BS = 86/83). Sequence differences between the two Stylidium plastomes were 5011 sites, including 2166 variable sites and 2845 indels, with the petA-psbJ spacer the most variable region, followed by the trnK UUU-matK intron and trnG UUG-rps16 spacer.
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Affiliation(s)
- Lin Li
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, China
| | - Guo-Ming Liu
- Chinese Carnivorous Plants Garden, Tongxiang, China
| | - Zhi-Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Richard T Corlett
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, China
| | - Wen-Bin Yu
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, China.,Southeast Asia Biodiversity Research Institute, Chinese Academy of Science, Nay Pyi Taw, Myanmar
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222
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Lyu R, He J, Luo Y, Lin L, Yao M, Cheng J, Xie L, Pei L, Yan S, Li L. Natural Hybrid Origin of the Controversial "Species" Clematis × pinnata (Ranunculaceae) Based on Multidisciplinary Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:745988. [PMID: 34712260 PMCID: PMC8545901 DOI: 10.3389/fpls.2021.745988] [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: 07/23/2021] [Accepted: 09/22/2021] [Indexed: 05/23/2023]
Abstract
Interspecific hybridization is common and has often been viewed as a driving force of plant diversity. However, it raises taxonomic problems and thus impacts biodiversity estimation and biological conservation. Although previous molecular phylogenetic studies suggested that interspecific hybridization may be rather common in Clematis, and artificial hybridization has been widely applied to produce new Clematis cultivars for nearly two centuries, the issue of natural hybridization of Clematis has never been addressed in detail. In this study, we tested the hybrid origin of a mesophytic and cold-adapted vine species, Clematis pinnata, which is a rare and taxonomically controversial taxon endemic to northern China. Using field investigations, flow cytometry (FCM), phylogenomic analysis, morphological statistics, and niche modeling, we tested hybrid origin and species status of C. pinnata. The FCM results showed that all the tested species were homoploid (2n = 16). Phylonet and HyDe analyses based on transcriptome data showed the hybrid origins of C. × pinnata from either C. brevicaudata × C. heracleifolia or C. brevicaudata × C. tubulosa. The plastome phylogeny depicted that C. × pinnata in different sampling sites originated by different hybridization events. Morphological analysis showed intermediacy of C. × pinnata between its putative parental species in many qualitative and quantitative characters. Niche modeling results suggested that C. × pinnata had not been adapted to a novel ecological niche independent of its putative parents. These findings demonstrated that plants of C. × pinnata did not formed a self-evolved clade and should not be treated as a species. The present study also suggests that interspecific hybridization is a common mechanism in Clematis to generate diversity and variation, and it may play an important role in the evolution and diversification of this genus. Our study implies that morphological diversity caused by natural hybridization may overstate the real species diversity in Clematis.
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Affiliation(s)
- Rudan Lyu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jian He
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Yike Luo
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lele Lin
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Min Yao
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Jin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Xie
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Linying Pei
- Beijing Engineering Research Center for Landscape Plant, Beijing Forestry University Forest Science Co. Ltd., Beijing, China
| | - Shuangxi Yan
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Liangqian Li
- Institute of Botany, The Chinese Academy of Sciences, Beijing, China
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223
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Pessoa EM, Ribeiro AC, Jud NA. A eudicot leaf from the Lower Cretaceous (Aptian, Araripe Basin) Crato Konservat-Lagerstätte. AMERICAN JOURNAL OF BOTANY 2021; 108:2055-2065. [PMID: 34647319 DOI: 10.1002/ajb2.1751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The Crato Konservat-Lagerstätte in Brazil preserves an exceptionally rich assemblage of plant macrofossils from the Early Cretaceous (late Aptian), including rare early angiosperm fossils related to Nymphaeales, monocots, and magnoliids, and a variety of angiosperms of uncertain affinities. Macrofossils of eudicot angiosperms have not been described previously, despite the presence of tricolpate pollen. We describe a fossil leaf with morphology characteristic of eudicot angiosperms. METHODS The fossil was collected from a quarry in the Lower Cretaceous (late Aptian) Crato Formation of northeastern Brazil in the state of Ceará. We compared the leaf architecture with that of ferns, gymnosperms, and similar living and fossil angiosperms. RESULTS The leaf of Baderadea pinnatissecta gen. et sp. nov. is simple and petiolate, with leaf architecture similar to that of some herbaceous Ranunculales. The blade is 5 cm long and the margin is untoothed and twice pinnately lobed with narrow lobes (pinnatisect). The primary vein framework is pinnate and there are multiple orders of reticulate venation. CONCLUSIONS The combination of characters preserved in the fossil supports the interpretation that B. pinnatissecta was an herbaceous eudicot similar to some members of Ranunculales and distinguished from other lobate Aptian angiosperms by leaf shape, presence of multiple orders of reticulate venation, and the absence of glandular teeth. The presence of eudicots in the flora of the Crato was already supported by pollen; the discovery of macrofossils like these provides additional information about their morphology and ecological role in low-latitude Early Cretaceous plant communities.
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Affiliation(s)
- Edlley M Pessoa
- Laboratório de Estudos Integrados de Plantas, Departamento de Botânica e Ecologia, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Alexandre C Ribeiro
- Departamento de Biologia e Zoologia, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Nathan A Jud
- Department of Biology, William Jewell College, Liberty, MO, 64068, USA
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224
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Du XY, Lu JM, Zhang LB, Wen J, Kuo LY, Mynssen CM, Schneider H, Li DZ. Simultaneous diversification of Polypodiales and angiosperms in the Mesozoic. Cladistics 2021; 37:518-539. [PMID: 34570931 DOI: 10.1111/cla.12457] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Comprising about 82% of the extant fern species diversity, Polypodiales are generally believed to have diversified in the Late Cretaceous. We estimated the divergence times of Polypodiales using both penalized likelihood and Bayesian methods, based on a dataset consisting of 208 plastomes representing all 28 families and 14 fossil constraints reflecting current interpretations of fossil record. Our plastome phylogeny recovered the same six major lineages as a recent nuclear phylogeny, but the position of Dennstaedtiineae was different. The present phylogeny showed high resolution of relationships among the families of Polypodiales, especially among those forming the Aspleniineae. The divergence time estimates supported the most recent common ancestor of Polypodiales and its closest relative dating back to the Triassic, establishment of the major lineages in the Jurassic, and a likely accelerated radiation during the late Jurassic and the Early Cretaceous. The estimated divergence patterns of Polypodiales and angiosperms converge to a scenario in which their main lineages were established simultaneously shortly before the onset of the Cretaceous Terrestrial Revolution, and further suggest a pre-Cretaceous hidden history for both lineages. The pattern of simultaneous diversifications shown here elucidate an important gap in our understanding of the Terrestrial Revolution that shaped today's ecosystems.
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Affiliation(s)
- Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
| | - Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO, 63110, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan, ROC
| | - Claudine M Mynssen
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Pacheco Leão 915, Rio de Janeiro, RJ, 22460-030, Brazil
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666000, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, Yunnan, 650201, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming, Yunnan, 650201, China
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225
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Moschin S, Nigris S, Ezquer I, Masiero S, Cagnin S, Cortese E, Colombo L, Casadoro G, Baldan B. Expression and Functional Analyses of Nymphaea caerulea MADS-Box Genes Contribute to Clarify the Complex Flower Patterning of Water Lilies. FRONTIERS IN PLANT SCIENCE 2021; 12:730270. [PMID: 34630477 PMCID: PMC8492926 DOI: 10.3389/fpls.2021.730270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Nymphaeaceae are early diverging angiosperms with large flowers characterized by showy petals and stamens not clearly whorled but presenting a gradual morphological transition from the outer elements to the inner stamens. Such flower structure makes these plant species relevant for studying flower evolution. MADS-domain transcription factors are crucial components of the molecular network that controls flower development. We therefore isolated and characterized MADS-box genes from the water lily Nymphaea caerulea. RNA-seq experiments on floral buds have been performed to obtain the transcript sequences of floral organ identity MADS-box genes. Maximum Likelihood phylogenetic analyses confirmed their belonging to specific MADS-box gene subfamilies. Their expression was quantified by RT-qPCR in all floral organs at two stages of development. Protein interactions among these transcription factors were investigated by yeast-two-hybrid assays. We found especially interesting the involvement of two different AGAMOUS-like genes (NycAG1 and NycAG2) in the water lily floral components. They were therefore functionally characterized by complementing Arabidopsis ag and shp1 shp2 mutants. The expression analysis of MADS-box genes across flower development in N. caerulea described a complex scenario made of numerous genes in numerous floral components. Their expression profiles in some cases were in line with what was expected from the ABC model of flower development and its extensions, while in other cases presented new and interesting gene expression patterns, as for instance the involvement of NycAGL6 and NycFL. Although sharing a high level of sequence similarity, the two AGAMOUS-like genes NycAG1 and NycAG2 could have undergone subfunctionalization or neofunctionalization, as only one of them could partially restore the euAG function in Arabidopsis ag-3 mutants. The hereby illustrated N. caerulea MADS-box gene expression pattern might mirror the morphological transition from the outer to the inner floral organs, and the presence of transition organs such as the petaloid stamens. This study is intended to broaden knowledge on the role and evolution of floral organ identity genes and the genetic mechanisms causing biodiversity in angiosperm flowers.
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Affiliation(s)
- Silvia Moschin
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Sebastiano Nigris
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Ignacio Ezquer
- Department of Biosciences, University of Milan, Milan, Italy
| | - Simona Masiero
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padua, Padua, Italy
- CRIBI Biotechnology Center, University of Padua, Padua, Italy
| | - Enrico Cortese
- Department of Biology, University of Padua, Padua, Italy
| | - Lucia Colombo
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Barbara Baldan
- Botanical Garden, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
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226
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Hong Z, Liao X, Ye Y, Zhang N, Yang Z, Zhu W, Gao W, Sharbrough J, Tembrock LR, Xu D, Wu Z. A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers. BMC Genomics 2021; 22:672. [PMID: 34536995 PMCID: PMC8449883 DOI: 10.1186/s12864-021-07967-7] [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: 04/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers. RESULTS We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome. CONCLUSION For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
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Affiliation(s)
- Zhou Hong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ningnan Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Zengjiang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Weidong Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.,College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Daping Xu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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227
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Leslie AB, Simpson C, Mander L. Reproductive innovations and pulsed rise in plant complexity. Science 2021; 373:1368-1372. [PMID: 34529461 DOI: 10.1126/science.abi6984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Andrew B Leslie
- Geological Sciences Department, Stanford University, 450 Jane Stanford Way, Building 320, Room 118, Stanford, CA 94305, USA
| | - Carl Simpson
- Geological Sciences, University of Colorado Museum of Natural History, University of Colorado Boulder, Campus Box 265, Boulder, CO 80304, USA
| | - Luke Mander
- School of Environment, Earth and Ecosystem Sciences, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK
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228
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Abstract
The evolutionary trajectories of insects and angiosperms appear to be intimately interconnected. Increases in the diversity of phytophagous beetles and angiosperms co-occur in the Mesozoic fossil record, and there is fossil evidence of pollinivory and pollination by insects, both in flowering plants and in gymnosperms. The oldest records of angiosperm pollination indicate flies as pollen vectors. A basal group of angiosperms, the order Magnoliales, has retained plesiomorphic characters such as dozens of pistils and stamens spiraling around the receptacle. In a family of this order, Annonaceae, over 90% of species are pollinated by beetles. In many Annonaceae species, flowers display wide spaces, referred to as floral chambers, where beetles can find shelter from weather conditions and predators, food in the form of pollen and tissues, and a mating site. Two basic types of floral chambers can be distinguished: small chambers visited by small beetles (Nitidulidae, Staphylinidae, Chrysomelidae, and Curculionidae) with diurnal and/or nocturnal activity and large and thermogenic floral chambers visited by beetles of the tribe Cyclocephalini (Scarabaeoidea, Melolonthidae). In the latter case, the heat that the flowers produce may serve as a resource for the beetles that visit them, resulting in smaller endothermy costs for the scarabs. This study reviewed the literature including PhD and MSc theses on cantharophilous Annonaceae in the Cerrado. In this biome, both types of associations are found, although cantharophilous Annonaceae represent a small portion of the plant species (<5%). Cantharophilous Annonaceae in the Cerrado share attributes according to the beetles that pollinate them: species pollinated by small beetles, for instance, may flower throughout the year, whereas Annonaceae pollinated by Cyclocephalini normally flower in the beginning of the rainy season (October/November), in synchrony with the phenological patterns of their pollinators. Cantharophilous Annonaceae flowers, regardless of their size, tend to have light colors and sweet and fruity odors. In addition to the lack of studies on the attraction of beetles by these floral characters, the taxonomic composition of the beetles that pollinate Annonaceae in the Cerrado is poorly known. This review attempts to discuss, in light of what has already been published, potential fields of investigation concerning pollinating beetles’ behavior and evolution.
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Ma H, Liu Y, Liu D, Sun W, Liu X, Wan Y, Zhang X, Zhang R, Yun Q, Wang J, Li Z, Ma Y. Chromosome-level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1533-1545. [PMID: 34189793 DOI: 10.1111/tpj.15399] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/23/2021] [Indexed: 05/25/2023]
Abstract
Rhododendrons are woody plants, famous throughout the world as having high horticultural value. However, many wild species are currently threatened with extinction. Here, we report for the first time a high-quality, chromosome-level genome of Rhododendron griersonianum, which has contributed to approximately 10% of all horticultural rhododendron varieties but which in its wild form has been evaluated as critically endangered. The final genome assembly, which has a contig N50 size of approximately 34 M and a total length of 677 M, is the highest-quality genome sequenced within the genus to date, in part due to its low heterozygosity (0.18%). Identified repeats constitute approximately 57% of the genome, and 38 280 protein-coding genes were predicted with high support. We further resequenced 31 individuals of R. griersonianum as well as 30 individuals of its widespread relative R. delavayi, and performed additional conservation genomic analysis. The results showed that R. griersonianum had lower genetic diversity (θ = 2.58e-3; π = 1.94e-3) when compared not only to R. delavayi (θ = 11.61e-3, π = 12.97e-3), but also to most other woody plants. Furthermore, three severe genetic bottlenecks were detected using both the Stairway plot and fastsimcoal2 analysis, which are thought to have occurred in the late Middle Pleistocene and the Last Glacial Maximum (LGM) period. After these bottlenecks, R. griersonianum recovered and maintained a constant effective population size (>25 000) until now. Intriguingly, R. griersonianum has accumulated significantly more deleterious mutations in the homozygous state than R. delavayi, and several deleterious mutations (e.g., in genes involved in the response to heat stress) are likely to have harmed the adaptation of this plant to its surroundings. This high-quality, chromosome-level genome and the population genomic analysis of the critically endangered R. griersonianum will provide an invaluable resource as well as insights for future study in this species to facilitate conservation and in the genus Rhododendron in general.
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Affiliation(s)
- Hong Ma
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xiongfang Liu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Youming Wan
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Xiujiao Zhang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Rengang Zhang
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Quanzheng Yun
- Beijing Ori-Gene Science and Technology Co. Ltd, Beijing, 102206, China
| | - Jihua Wang
- The Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China
- National Engineering Research Center for Ornamental Horticulture, Kunming, 650205, China
| | - Zhenghong Li
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Qin L, Hu Y, Wang J, Wang X, Zhao R, Shan H, Li K, Xu P, Wu H, Yan X, Liu L, Yi X, Wanke S, Bowers JE, Leebens-Mack JH, dePamphilis CW, Soltis PS, Soltis DE, Kong H, Jiao Y. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. NATURE PLANTS 2021; 7:1239-1253. [PMID: 34475528 PMCID: PMC8445822 DOI: 10.1038/s41477-021-00990-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 07/22/2021] [Indexed: 05/04/2023]
Abstract
Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.
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Affiliation(s)
- Liuyu Qin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Hu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinpeng Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoliang Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Kunpeng Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanying Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lumei Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Yi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Stefan Wanke
- Institute of Botany, Dresden University of Technology, Dresden, Germany
| | - John E Bowers
- Department of Plant Biology, University of Georgia, Athens, GA, USA
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
| | | | - Claude W dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Ruiz-Hernández V, Joubert L, Rodríguez-Gómez A, Artuso S, Pattrick JG, Gómez PA, Eckerstorfer S, Brandauer SS, Trcka-Rojas CGI, Martínez-Reina L, Booth J, Lau-Zhu A, Weiss J, Bielza P, Glover BJ, Junker RR, Egea-Cortines M. Humans Share More Preferences for Floral Phenotypes With Pollinators Than With Pests. FRONTIERS IN PLANT SCIENCE 2021; 12:647347. [PMID: 34497617 PMCID: PMC8419516 DOI: 10.3389/fpls.2021.647347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Studies on the selection of floral traits usually consider pollinators and sometimes herbivores. However, humans also exert selection on floral traits of ornamental plants. We compared the preferences of bumblebees (Bombus terrestris), thrips (Frankliniella occidentalis), and humans for flowers of snapdragon. From a cross of two species, Antirrhinum majus and Antirrhinum linkianum, we selected four Recombinant Inbred Lines (RILs). We characterised scent emission from whole flowers and stamens, pollen content and viability, trichome density, floral shape, size and colour of floral parts. We tested the preferences of bumblebees, thrips, and humans for whole flowers, floral scent bouquets, stamen scent, and individual scent compounds. Humans and bumblebees showed preferences for parental species, whereas thrips preferred RILs. Colour and floral scent, in combination with other floral traits, seem relevant phenotypes for all organisms. Remarkably, visual traits override scent cues for bumblebees, although, scent is an important trait when bumblebees cannot see the flowers, and methyl benzoate was identified as a key attractant for them. The evolutionary trajectory of flowers is the result of multiple floral traits interacting with different organisms with different habits and modes of interaction.
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Affiliation(s)
- Victoria Ruiz-Hernández
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Cartagena, Cartagena, Spain
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Biosciences, University Salzburg, Salzburg, Austria
| | - Lize Joubert
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Amador Rodríguez-Gómez
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Silvia Artuso
- Department of Biosciences, University Salzburg, Salzburg, Austria
| | - Jonathan G. Pattrick
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Perla A. Gómez
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
| | | | | | | | - Luis Martínez-Reina
- Departamento de Arquitectura y Tecnología de la Edificación, Escuela Técnica Superior de Arquitectura y Edificación, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Josh Booth
- Department of Sociology, University of Cambridge, Cambridge, United Kingdom
| | - Alex Lau-Zhu
- Oxford Institute of Clinical Psychology Training and Research, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
- Division of Psychiatry, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Julia Weiss
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Pablo Bielza
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Beverley J. Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Robert R. Junker
- Department of Biosciences, University Salzburg, Salzburg, Austria
- Evolutionary Ecology of Plants, Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Marcos Egea-Cortines
- Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Edificio I+D+I, Campus Muralla del Mar, Cartagena, Spain
- Departamento de Ingeniería Agronómica, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Cartagena, Cartagena, Spain
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Mehl T, Gruenstaeudl M. airpg: automatically accessing the inverted repeats of archived plastid genomes. BMC Bioinformatics 2021; 22:413. [PMID: 34418956 PMCID: PMC8379869 DOI: 10.1186/s12859-021-04309-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. RESULTS We introduce airpg, a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using airpg, followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. CONCLUSION The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. airpg enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg .
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Affiliation(s)
- Tilman Mehl
- Institut für Bioinformatik, Freie Universität Berlin, 14195 Berlin, Germany
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233
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Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics. Mol Phylogenet Evol 2021; 164:107287. [PMID: 34365014 DOI: 10.1016/j.ympev.2021.107287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
Lamiales is one of the most intractable orders of flowering plants, with several changes in family composition, and circumscription throughout history. The order is worldwide distributed, occurring in tropical forests and frozen habitats. In this study, a comprehensive phylogeny of Lamiales was reconstructed using DNA sequences. The tree was used to infer dispersal patterns, focusing on the tropics and extratropics. Molecular and species geographic data available from public repositories were combined to address both objectives. A total of 6,910 species, and 842 genera of Lamiales were sampled using the Python tool PyPHLAWD. The tree was inferred using RAxML, and recovered a monophyletic Lamiales. All 26 families were recovered as monophyletic with high support. The families Bignoniaceae, and Plantaginaceae are remarkable examples. The first emerged as monophyletic and included tribe Jacarandeae, while the later emerged as monophyletic in its sensu lato and included both the tribes Angelonieae, and Gratioleae. Distribution points for all species were retrieved from GBIF. After filtering, 1,136,425 records were retained. Species were coded as present in extratropical or tropical environments. The in and out of the tropics dispersal patterns were inferred using a maximum likelihood approach that identifies hidden rate changes. The model recovered higher rates of transition from extratropics to tropics, estimating two rates of state transitions. When ancestral states are considered, more discrete transitions from extratropics to tropics were observed. The extratropical state was also inferred for the crown node of Lamiales and old nested nodes, revealing a rare pattern of transitions to the tropics throughout the upper Cretaceous and Tertiary. A significant phylogenetic signal was recovered for the in and out of the tropics dispersal patterns, showing that state transitions are not frequent enough to erase the effect of tree structure on the data.
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234
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Yao N, Schmitz RJ, Johannes F. Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021; 37:699-710. [PMID: 34016450 PMCID: PMC8282728 DOI: 10.1016/j.tig.2021.04.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/16/2022]
Abstract
Stochastic gains and losses of DNA methylation at CG dinucleotides are a frequent occurrence in plants. These spontaneous 'epimutations' occur at a rate that is 100 000 times higher than the genetic mutation rate, are effectively neutral at the genome-wide scale, and are stably inherited across mitotic and meiotic cell divisions. Mathematical models have been extraordinarily successful at describing how epimutations accumulate in plant genomes over time, making this process one of the most predictable epigenetic phenomena to date. Here, we propose that their high rate and effective neutrality make epimutations a powerful new molecular clock for timing evolutionary events of the recent past and for age dating of long-lived perennials such as trees.
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Affiliation(s)
- Nan Yao
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, USA; Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Frank Johannes
- Institute for Advanced Study, Technical University of Munich, Garching, Germany; Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.
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An updated phylogenetic and biogeographic analysis based on genome skimming data reveals convergent evolution of shrubby habit in Clematis in the Pliocene and Pleistocene. Mol Phylogenet Evol 2021; 164:107259. [PMID: 34303792 DOI: 10.1016/j.ympev.2021.107259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
Abstract
Convergent evolution, often viewed as the inevitable outcome of natural selection, has received special attention since the time of Darwin. Clematis is well known for its climbing habit, but it has some shrubby species, known as sect. Fruticella s.l. The shrubby Clematis species are distributed in the dry habitats of Central Asia and adjacent areas showing possible convergent evolution. In this study, we assembled the complete plastome and nuclear ribosomal DNA (nrDNA) sequences of 56 Clematis species, representing most sections and covering most of the shrubby species, to reconstruct their evolutionary histories. Using both maximum likelihood and Bayesian methods, the plastome and nrDNA datasets generated similar, but not identical, phylogenetic relationships, which are better resolved than in previous studies. Then, molecular dating, historical range reconstruction, and character optimization analyses were conducted based on this updated phylogenetic framework. All the morphological characters widely used for taxonomy were shown to have evolved multiple times. Molecular dating inferred that Clematis diverged from its sister in the mid Miocene, and all six major clades of Clematis originated during the late Miocene, with a species radiation during the Pliocene to Pleistocene. The results clearly showed that the shrubby habit evolved independently in four lineages of Clematis in Asia. We also revealed that the shrubby lineages have emerged since the very beginning of Pliocene. Asian monsoon variation in the Pliocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby Clematis in Central Asia and adjacent dry areas.
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Jin L, Liu JJ, Xiao TW, Li QM, Lin LX, Shao XN, Ma CX, Li BH, Mi XC, Ren HB, Qiao XJ, Lian JY, Hao G, Ge XJ. Plastome-based phylogeny improves community phylogenetics of subtropical forests in China. Mol Ecol Resour 2021; 22:319-333. [PMID: 34233085 DOI: 10.1111/1755-0998.13462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.
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Affiliation(s)
- Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Na Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chen-Xin Ma
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bu-Hang Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiang-Cheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hai-Bao Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Juan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Ju-Yu Lian
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Gang Hao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Lee AK, Gilman IS, Srivastav M, Lerner AD, Donoghue MJ, Clement WL. Reconstructing Dipsacales phylogeny using Angiosperms353: issues and insights. AMERICAN JOURNAL OF BOTANY 2021; 108:1122-1142. [PMID: 34254290 PMCID: PMC8362060 DOI: 10.1002/ajb2.1695] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/12/2021] [Indexed: 05/04/2023]
Abstract
PREMISE Phylogenetic relationships within major angiosperm clades are increasingly well resolved, but largely informed by plastid data. Areas of poor resolution persist within the Dipsacales, including placement of Heptacodium and Zabelia, and relationships within the Caprifolieae and Linnaeeae, hindering our interpretation of morphological evolution. Here, we sampled a significant number of nuclear loci using a Hyb-Seq approach and used these data to infer the Dipsacales phylogeny and estimate divergence times. METHODS Sampling all major clades within the Dipsacales, we applied the Angiosperms353 probe set to 96 species. Data were filtered based on locus completeness and taxon recovery per locus, and trees were inferred using RAxML and ASTRAL. Plastid loci were assembled from off-target reads, and 10 fossils were used to calibrate dated trees. RESULTS Varying numbers of targeted loci and off-target plastomes were recovered from most taxa. Nuclear and plastid data confidently place Heptacodium with Caprifolieae, implying homoplasy in calyx morphology, ovary development, and fruit type. Placement of Zabelia, and relationships within the Caprifolieae and Linnaeeae, remain uncertain. Dipsacales diversification began earlier than suggested by previous angiosperm-wide dating analyses, but many major splitting events date to the Eocene. CONCLUSIONS The Angiosperms353 probe set facilitated the assembly of a large, single-copy nuclear dataset for the Dipsacales. Nevertheless, many relationships remain unresolved, and resolution was poor for woody clades with low rates of molecular evolution. We favor expanding the Angiosperms353 probe set to include more variable loci and loci of special interest, such as developmental genes, within particular clades.
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Affiliation(s)
- Aaron K. Lee
- Department of BiologyThe College of New JerseyEwingNJ08628USA
- Department of Plant and Microbial BiologyUniversity of Minnesota ‐ Twin CitiesSaint PaulMN55108USA
| | - Ian S. Gilman
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Mansa Srivastav
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Ariel D. Lerner
- Department of BiologyThe College of New JerseyEwingNJ08628USA
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. AMERICAN JOURNAL OF BOTANY 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. AMERICAN JOURNAL OF BOTANY 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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240
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. AMERICAN JOURNAL OF BOTANY 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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241
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Maurin O, Anest A, Bellot S, Biffin E, Brewer G, Charles-Dominique T, Cowan RS, Dodsworth S, Epitawalage N, Gallego B, Giaretta A, Goldenberg R, Gonçalves DJP, Graham S, Hoch P, Mazine F, Low YW, McGinnie C, Michelangeli FA, Morris S, Penneys DS, Pérez Escobar OA, Pillon Y, Pokorny L, Shimizu G, Staggemeier VG, Thornhill AH, Tomlinson KW, Turner IM, Vasconcelos T, Wilson PG, Zuntini AR, Baker WJ, Forest F, Lucas E. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. AMERICAN JOURNAL OF BOTANY 2021; 108:1087-1111. [PMID: 34297852 DOI: 10.1002/ajb2.1699] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
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Affiliation(s)
- Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Artemis Anest
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Edward Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Tristan Charles-Dominique
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil
| | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | | | - Peter Hoch
- Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Fiorella Mazine
- Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil
| | - Yee Wen Low
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | | | - Fabián A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | | | - Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Gustavo Shimizu
- Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | - Andrew H Thornhill
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Ian M Turner
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Peter G Wilson
- Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Peris D, Delclòs X, Jordal B. Origin and evolution of fungus farming in wood-boring Coleoptera - a palaeontological perspective. Biol Rev Camb Philos Soc 2021; 96:2476-2488. [PMID: 34159702 DOI: 10.1111/brv.12763] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Insect-fungus mutualism is one of the better-studied symbiotic interactions in nature. Ambrosia fungi are an ecological assemblage of unrelated fungi that are cultivated by ambrosia beetles in their galleries as obligate food for larvae. Despite recently increased research interest, it remains unclear which ecological factors facilitated the origin of fungus farming, and how it transformed into a symbiotic relationship with obligate dependency. It is clear from phylogenetic analyses that this symbiosis evolved independently many times in several beetle and fungus lineages. However, there is a mismatch between palaeontological and phylogenetic data. Herein we review, for the first time, the ambrosia system from a palaeontological perspective. Although largely ignored, families such as Lymexylidae and Bostrichidae should be included in the list of ambrosia beetles because some of their species cultivate ambrosia fungi. The estimated origin for some groups of ambrosia fungi during the Cretaceous concurs with a known high diversity of Lymexylidae and Bostrichidae at that time. Although potentially older, the greatest radiation of various ambrosia beetle lineages occurred in the weevil subfamilies Scolytinae and Platypodinae during the Eocene. In this review we explore the evolutionary relationship between ambrosia beetles, fungi and their host trees, which is likely to have persisted for longer than previously supposed.
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Affiliation(s)
- David Peris
- Institute of Geosciences, University of Bonn, Nussallee 8, Bonn, 53115, Germany.,Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Martí i Franquès s/n, Barcelona, 08028, Spain
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics, Faculty of Earth Sciences, University of Barcelona, Martí i Franquès s/n, Barcelona, 08028, Spain.,Biodiversity Research Institute (IRBio), University of Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
| | - Bjarte Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Haakon Sheteligs plass 10, Bergen, N-5007, Norway
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243
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Kania-Kłosok I, Krzemiński W, Arillo A. Two new long-rostrum cranefly species from the Cretaceous Iberian amber (Diptera, Limoniidae, Helius). Sci Rep 2021; 11:12851. [PMID: 34145304 PMCID: PMC8213732 DOI: 10.1038/s41598-021-91803-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/01/2021] [Indexed: 12/04/2022] Open
Abstract
First record of the genus Helius-long-rostrum cranefly from Maestrazgo Basin (eastern Spain, Iberian Penisula) is documented. Two new fossil species of the genus Helius are described from Cretaceous Spanish amber and compared with other species of the genus known from fossil record with particular references to these known from Cretaceous period. Helius turolensis sp. nov. is described from San Just amber (Lower Cretaceous, upper Albian) Maestrazgo Basin, eastern Spain, and Helius hispanicus sp. nov. is described from Álava amber (Lower Cretaceous, upper Albian), Basque-Cantabrian Basin, northern Spain. The specific body morphology of representatives of the genus Helius preserved in Spanish amber was discussed in relation to the environmental conditions of the Maestrazgo Basin and Basque-Cantabrian Basin in Cretaceous.
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Affiliation(s)
- Iwona Kania-Kłosok
- Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszów, Zelwerowicza 4, 35-601, Rzeszów, Poland.
| | - Wiesław Krzemiński
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Antonio Arillo
- Departamento de Biodiversidad, Facultad de Biología, Ecología y Evolución, Universidad Complutense, 28040, Madrid, Spain
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Li J, Price M, Su DM, Zhang Z, Yu Y, Xie DF, Zhou SD, He XJ, Gao XF. Phylogeny and Comparative Analysis for the Plastid Genomes of Five Tulipa (Liliaceae). BIOMED RESEARCH INTERNATIONAL 2021; 2021:6648429. [PMID: 34239930 PMCID: PMC8235973 DOI: 10.1155/2021/6648429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Species of Tulipa (Liliaceae) are of great horticultural importance and are distributed across Europe, North Africa, and Asia. The Tien Shan Mountain is one of the primary diversity centres of Tulipa, but the molecular studies of Tulipa species from this location are lacking. In our study, we assembled four Tulipa plastid genomes from the Tien Shan Mountains, T. altaica, T. iliensis, T. patens, and T. thianschanica, combined with the plastid genome of T. sylvestris to compare against other Liliaceae plastid genomes. We focussed on the species diversity and evolution of their plastid genomes. The five Tulipa plastid genomes proved highly similar in overall size (151,691-152,088 bp), structure, gene order, and content. With comparative analysis, we chose 7 mononucleotide SSRs from the Tulipa species that could be used in further population studies. Phylogenetic analyses based on 24 plastid genomes robustly supported the monophyly of Tulipa and the sister relationship between Tulipa and Amana, Erythronium. T. iliensis, T. thianschanica, and T. altaica were clustered together, and T. patens was clustered with T. sylvestris, with our results clearly demonstrating the relationships between these five Tulipa species. Our results provide a more comprehensive understanding of the phylogenomics and comparative genomics of Tulipa.
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Affiliation(s)
- Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Dan-Mei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 Sichuan, China
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Rosas-Reinhold I, Piñeyro-Nelson A, Rosas U, Arias S. Blurring the Boundaries between a Branch and a Flower: Potential Developmental Venues in CACTACEAE. PLANTS (BASEL, SWITZERLAND) 2021; 10:1134. [PMID: 34204904 PMCID: PMC8228900 DOI: 10.3390/plants10061134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
Flowers are defined as short shoots that carry reproductive organs. In Cactaceae, this term acquires another meaning, since the flower is interpreted as a branch with a perianth at the tip, with all reproductive organs embedded within the branch, thus giving way to a structure that has been called a "flower shoot". These organs have long attracted the attention of botanists and cactologists; however, the understanding of the morphogenetic processes during the development of these structures is far from clear. In this review, we present and discuss some classic flower concepts used to define floral structures in Cactaceae in the context of current advances in flower developmental genetics and evolution. Finally, we propose several hypotheses to explain the origin of these floral shoot structures in cacti, and we suggest future research approaches and methods that could be used to fill the gaps in our knowledge regarding the ontogenetic origin of the "flower" in the cactus family.
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Affiliation(s)
- Isaura Rosas-Reinhold
- Instituto de Biología, Jardín Botánico, Universidad Nacional Autónoma de México, Ciudad de México C.P.04510, Mexico; (I.R.-R.); (U.R.)
- Posgrado en Ciencias Biológicas, Instituto de Biología, Universidad Nacional Autónoma de México, A. P. 70-153, Ciudad de México C.P.04510, Mexico
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México C.P.04510, Mexico;
- Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad de México C.P.04960, Mexico
| | - Ulises Rosas
- Instituto de Biología, Jardín Botánico, Universidad Nacional Autónoma de México, Ciudad de México C.P.04510, Mexico; (I.R.-R.); (U.R.)
| | - Salvador Arias
- Instituto de Biología, Jardín Botánico, Universidad Nacional Autónoma de México, Ciudad de México C.P.04510, Mexico; (I.R.-R.); (U.R.)
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Niu G, Jiang S, Doğan Ö, Korkmaz EM, Budak M, Wu D, Wei M. Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily. INSECTS 2021; 12:495. [PMID: 34073280 PMCID: PMC8227683 DOI: 10.3390/insects12060495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.
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Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
| | - Sijia Jiang
- College of Forestry, Beijing Forestry University, Beijing 100083, China;
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Duo Wu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
| | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
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247
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Zhang XF, Landis JB, Wang HX, Zhu ZX, Wang HF. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC PLANT BIOLOGY 2021; 21:219. [PMID: 33992095 PMCID: PMC8122561 DOI: 10.1186/s12870-021-02985-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. RESULTS A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214-171,315 bp and exhibit a typical four part structure. The IR region is between 23,901-36,747 bp, with the large single copy region spanning 83,691-91,249 bp and the small single copy region spanning 11,150-19,703 bp. In total, 123-133 genes are present in the chloroplasts including 77-81 protein coding genes, four rRNA genes and 30-31 tRNA genes. The GC content was 36.9-38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7-37.3%, 30.6-36.8% and 39.7-43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88-114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50-118.62 Ma). CONCLUSIONS The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.
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Affiliation(s)
- Xiao-Feng Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Hong-Xin Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Zhi-Xin Zhu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Hua-Feng Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.
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248
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Barba-Montoya J, Tao Q, Kumar S. Molecular and morphological clocks for estimating evolutionary divergence times. BMC Ecol Evol 2021; 21:83. [PMID: 33980146 PMCID: PMC8117668 DOI: 10.1186/s12862-021-01798-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. RESULTS We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as some intermediate nodes may show large time differences between these two types of data. CONCLUSIONS Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.
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Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
- Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia.
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249
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de Vries S, de Vries J. Plant Genome Evolution: Meat Lovers Expanded Gene Families for Carnivory and Dropped the Rest. Curr Biol 2021; 30:R700-R702. [PMID: 32574630 DOI: 10.1016/j.cub.2020.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Every textbook says that land plants are primary producers and, as such, are eaten. A couple of plants, however, refuse to stay within the boundaries of their trophic level - the carnivorous plants. Now, a new genomic study pinpoints the genetic chassis that underpins carnivory in Venus flytrap, waterwheel plant, and sundew.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
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250
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Chua PYS, Crampton-Platt A, Lammers Y, Alsos IG, Boessenkool S, Bohmann K. Metagenomics: A viable tool for reconstructing herbivore diet. Mol Ecol Resour 2021; 21:2249-2263. [PMID: 33971086 PMCID: PMC8518049 DOI: 10.1111/1755-0998.13425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/08/2021] [Accepted: 05/04/2021] [Indexed: 11/28/2022]
Abstract
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
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Affiliation(s)
- Physilia Y S Chua
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Youri Lammers
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Inger G Alsos
- Tromsø Museum, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Sanne Boessenkool
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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