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Mihaminekena TH, Rakotonanahary AN, Frasier CL, Randriahaingo HNT, Sefczek TM, Tinsman J, Randrianarimanana HL, Ravaloharimanitra M, Rakotoarinivo TH, Ratsimbazafy J, King T, Louis EE. Dietary flexibility of the greater bamboo lemur (Prolemur simus), a specialized feeder, in eastern Madagascar. Am J Primatol 2024; 86:e23609. [PMID: 38409820 DOI: 10.1002/ajp.23609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 01/23/2024] [Accepted: 02/10/2024] [Indexed: 02/28/2024]
Abstract
The degree of dietary flexibility in primates is species specific; some incorporate a wider array of resources than others. Extreme interannual weather variability in Madagascar results in seasonal resource scarcity which has been linked to specialized behaviors in lemurs. Prolemur simus, for example, has been considered an obligate specialist on large culm bamboo with >60% of its diet composed of woody bamboos requiring morphological and physiological adaptations to process. Recent studies reported an ever-expanding list of dietary items, suggesting that this species may not be an obligate specialist. However, long-term quantitative feeding data are unavailable across this species' range. To explore the dietary flexibility of P. simus, we collected data at two northern sites, Ambalafary and Sahavola, and one southern site, Vatovavy, from September 2010 to January 2016 and May 2017 to September 2018, respectively. In total, we recorded 4022 h of behavioral data using instantaneous sampling of adult males and females from one group in Ambalafary, and two groups each in Sahavola and Vatovavy. We recorded 45 plant species eaten by P. simus over 7 years. We also observed significant differences in seasonal dietary composition between study sites. In Ambalafary, bamboo was the most frequently observed resource consumed (92.2%); however, non-bamboo resources comprised nearly one-third of the diet of P. simus in Sahavola and over 60% in Vatovavy. Consumption of all bamboo resources increased during the dry season at Ambalafary and during the wet season at Vatovavy, but never exceeded non-bamboo feeding at the latter. Culm pith feeding was only observed at Ambalafary, where it was more common during the dry season. We identify P. simus as a bamboo facultative specialist capable of adjusting its feeding behavior to its environment, indicating greater dietary flexibility than previously documented, which may enable the species to survive in increasingly degraded habitats.
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Affiliation(s)
- T Hasimija Mihaminekena
- The Aspinall Foundation Madagascar Programme, Antananarivo, Madagascar
- Zoologie et Anthropologie Biologique, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ando N Rakotonanahary
- Mention Science de la Vie et de l'Environnement, Faculté des Sciences de Technologie et de l'Environnement (FSTE), Université de Mahajanga, Mahajanga, Madagascar
- Madagascar Biodiversity Partnership NGO (MBP), Antananarivo, Madagascar
| | - Cynthia L Frasier
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | | | - Timothy M Sefczek
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
- School of Global Integrative Studies, University of Nebraska, Lincoln, Nebraska, USA
| | - Jen Tinsman
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
| | | | | | | | - Jonah Ratsimbazafy
- Groupe d'Etude et de Recherche sur les Primates (GERP), Antananarivo, Madagascar
| | - Tony King
- The Aspinall Foundation Madagascar Programme, Antananarivo, Madagascar
- The Aspinall Foundation, Port Lympne Reserve, Kent, UK
- School of Anthropology and Conservation, Durrell Institute of Conservation and Ecology, University of Kent, Kent, UK
| | - Edward E Louis
- Madagascar Biodiversity Partnership NGO (MBP), Antananarivo, Madagascar
- Conservation Genetics Department, Omaha's Henry Doorly Zoo and Aquarium, Omaha, Nebraska, USA
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Yao G, Zhang YQ, Barrett C, Xue B, Bellot S, Baker WJ, Ge XJ. A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol 2023; 21:50. [PMID: 36882831 PMCID: PMC9993706 DOI: 10.1186/s12915-023-01544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research. RESULTS Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support. CONCLUSIONS The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
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Affiliation(s)
- Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Present Address: College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
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Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Mo ZQ, Fu CN, Zhu MS, Milne RI, Yang JB, Cai J, Qin HT, Zheng W, Hollingsworth PM, Li DZ, Gao LM. Resolution, conflict and rate shifts: insights from a densely sampled plastome phylogeny for Rhododendron (Ericaceae). ANNALS OF BOTANY 2022; 130:687-701. [PMID: 36087101 PMCID: PMC9670778 DOI: 10.1093/aob/mcac114] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Rhododendron is a species-rich and taxonomically challenging genus due to recent adaptive radiation and frequent hybridization. A well-resolved phylogenetic tree would help to understand the diverse history of Rhododendron in the Himalaya-Hengduan Mountains where the genus is most diverse. METHODS We reconstructed the phylogeny based on plastid genomes with broad taxon sampling, covering 161 species representing all eight subgenera and all 12 sections, including ~45 % of the Rhododendron species native to the Himalaya-Hengduan Mountains. We compared this phylogeny with nuclear phylogenies to elucidate reticulate evolutionary events and clarify relationships at all levels within the genus. We also estimated the timing and diversification history of Rhododendron, especially the two species-rich subgenera Rhododendron and Hymenanthes that comprise >90 % of Rhododendron species in the Himalaya-Hengduan Mountains. KEY RESULTS The full plastid dataset produced a well-resolved and supported phylogeny of Rhododendron. We identified 13 clades that were almost always monophyletic across all published phylogenies. The conflicts between nuclear and plastid phylogenies suggested strongly that reticulation events may have occurred in the deep lineage history of the genus. Within Rhododendron, subgenus Therorhodion diverged first at 56 Mya, then a burst of diversification occurred from 23.8 to 17.6 Mya, generating ten lineages among the component 12 clades of core Rhododendron. Diversification in subgenus Rhododendron accelerated c. 16.6 Mya and then became fairly continuous. Conversely, Hymenanthes diversification was slow at first, then accelerated very rapidly around 5 Mya. In the Himalaya-Hengduan Mountains, subgenus Rhododendron contained one major clade adapted to high altitudes and another to low altitudes, whereas most clades in Hymenanthes contained both low- and high-altitude species, indicating greater ecological plasticity during its diversification. CONCLUSIONS The 13 clades proposed here may help to identify specific ancient hybridization events. This study will help to establish a stable and reliable taxonomic framework for Rhododendron, and provides insight into what drove its diversification and ecological adaption. Denser sampling of taxa, examining both organelle and nuclear genomes, is needed to better understand the divergence and diversification history of Rhododendron.
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Affiliation(s)
| | | | - Ming-Shu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, 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
| | - Han-Tao Qin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
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Buitrago Acosta MC, Montúfar R, Guyot R, Mariac C, Tranbarger TJ, Restrepo S, Couvreur TLP. Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1540-1544. [PMID: 36046105 PMCID: PMC9423826 DOI: 10.1080/23802359.2022.2109437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.
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Affiliation(s)
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Romain Guyot
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Cedric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Thomas L. P. Couvreur
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Francisconi AF, Cauz-Santos LA, Morales Marroquín JA, van den Berg C, Alves-Pereira A, Delmondes de Alencar L, Picanço-Rodrigues D, Zanello CA, Ferreira Costa M, Gomes Lopes MT, Veasey EA, Zucchi MI. Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes. PLoS One 2022; 17:e0266304. [PMID: 35901127 PMCID: PMC9333295 DOI: 10.1371/journal.pone.0266304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
| | | | | | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brasil
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Luciano Delmondes de Alencar
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Cesar Augusto Zanello
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Marcones Ferreira Costa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, Floriano, Piauí, Brasil
| | - Maria Teresa Gomes Lopes
- Departamento de Produção Animal e Vegetal, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Maria Imaculada Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
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Jiang H, Tian J, Yang J, Dong X, Zhong Z, Mwachala G, Zhang C, Hu G, Wang Q. Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences. BMC PLANT BIOLOGY 2022; 22:177. [PMID: 35387599 PMCID: PMC8985347 DOI: 10.1186/s12870-022-03529-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/14/2022] [Indexed: 05/22/2023]
Abstract
BACKGROUND Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species. RESULTS The results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9-37.0%. Gene annotation revealed 106-109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust. CONCLUSIONS Our study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.
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Affiliation(s)
- Hui Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Tian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jiaxin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhixiang Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Geoffrey Mwachala
- East African Herbarium, National Museums of Kenya, P.O. Box 45166, Nairobi, 00100, Kenya
| | - Caifei Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Qingfeng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Li J, Cai J, Qin HH, Price M, Zhang Z, Yu Y, Xie DF, He XJ, Zhou SD, Gao XF. Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 12:699226. [PMID: 35178055 PMCID: PMC8845482 DOI: 10.3389/fpls.2021.699226] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 12/08/2021] [Indexed: 05/16/2023]
Abstract
Tribe Lilieae, encompassing Lilium, Notholirion, Cardiocrinum, and Fritillaria, includes economically important crops with a horticultural and medicinal value. It is considered to be a core lineage of Liliaceae, but phylogenetic relationships within it, and the timing of the origin of individual clades, remain incompletely resolved. To address these issues, we reconstructed the evolutionary history of the tribe. We sequenced 45 Liliaceae plastomes and combined them with publicly available data (for a total of 139 plastomes) to explore the systematics, origin, divergence, and evolution of Lilieae. Our taxon sampling covers all ten sections of Lilium, all Cardiocrinum species, three Notholirion species, and major phylogenetic clades of Fritillaria. Our phylogenetic analysis confirms the monophyly of major sections/subgenera of Lilium and Fritillaria with strong support. We dated the origin of Lilieae to the Eocene, with genera and species radiations inferred to have occurred in the Miocene. The reconstruction of the ancestral area implies that Lilieae may have originated from the Qinghai-Tibet Plateau (QTP): the Himalayas and Hengduan Mountains and uplifting of the QTP likely promoted divergence within the tribe. Ancestral-state reconstructions of the bulb component number (including bulblets and scales) show a strong correlation with the genus-level phylogenetic diversity in Lilieae. They also predict that the most recent common ancestor of Lilieae had bulbs with numerous bulblets. Based on these observations, we predicted that climatic oscillations associated with the QTP uplift played an important role in the evolution of the Lilieae bulb. Our findings provide a well-supported picture of evolutionary relationships and a useful framework for understanding the pathway of bulb evolution within Lilieae, contributing to a better understanding of the evolutionary history of lilies.
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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, China
| | - Jing Cai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huan-Huan Qin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Megan Price
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Deng-Feng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 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, China
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10
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Wu H, Yang JB, Liu JX, Li DZ, Ma PF. Organelle Phylogenomics and Extensive Conflicting Phylogenetic Signals in the Monocot Order Poales. FRONTIERS IN PLANT SCIENCE 2022; 12:824672. [PMID: 35173754 PMCID: PMC8841755 DOI: 10.3389/fpls.2021.824672] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The Poales is one of the largest orders of flowering plants with significant economic and ecological values. Reconstructing the phylogeny of the Poales is important for understanding its evolutionary history that forms the basis for biological studies. However, due to sparse taxon sampling and limited molecular data, previous studies have resulted in a variety of contradictory topologies. In particular, there are three nodes surrounded by incongruence: the phylogenetic ambiguity near the root of the Poales tree, the sister family of Poaceae, and the delimitation of the xyrid clade. We conducted a comprehensive sampling and reconstructed the phylogenetic tree using plastid and mitochondrial genomic data from 91 to 66 taxa, respectively, representing all the 16 families of Poales. Our analyses support the finding of Bromeliaceae and Typhaceae as the earliest diverging groups within the Poales while having phylogenetic relationships with the polytomy. The clade of Ecdeiocoleaceae and Joinvilleaceae is recovered as the sister group of Poaceae. The three families, Mayacaceae, Eriocaulaceae, and Xyridaceae, of the xyrid assembly diverged successively along the backbone of the Poales phylogeny, and thus this assembly is paraphyletic. Surprisingly, we find substantial phylogenetic conflicts within the plastid genomes of the Poales, as well as among the plastid, mitochondrial, and nuclear data. These conflicts suggest that the Poales could have a complicated evolutionary history, such as rapid radiation and polyploidy, particularly allopolyploidy through hybridization. In sum, our study presents a new perspicacity into the complex phylogenetic relationships and the underlying phylogenetic conflicts within the Poales.
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Affiliation(s)
- Hong Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jing-Xia Liu
- 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
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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11
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Huang Y, Fan L, Huang J, Zhou G, Chen X, Chen J. Plastome Phylogenomics of Aucuba (Garryaceae). Front Genet 2022; 13:753719. [PMID: 35140747 PMCID: PMC8819091 DOI: 10.3389/fgene.2022.753719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/04/2022] [Indexed: 12/25/2022] Open
Abstract
Aucuba (Garryaceae), which includes approximately ten evergreen woody species, is a genus endemic to East Asia. Their striking morphological features give Aucuba species remarkable ornamental value. Owing to high levels of morphological divergence and plasticity, species definitions of Aucuba remain perplexing and problematic. Here, we sequenced and characterized the complete plastid genomes (plastomes) of three Aucuba species: Aucuba chlorascens, Aucuba eriobotryifolia, and Aucuba japonica. Incorporating Aucuba plastomes available in GenBank, a total of seven Aucuba plastomes, representing six out of ten species of Aucuba, were used for comparative plastome analysis, phylogenetic analysis and divergence time estimation in this study. Comparative analyses revealed that plastomes of Aucuba are highly conserved in size, structure, gene content, and organization, and exhibit high levels of sequence similarity. Phylogenetic reconstruction based on 68 plastid protein-coding genes strongly supported the monophyly of Garryales, Garryaceae and Aucuba. Aucuba eriobotryifolia was sister to the other Aucuba species examined, consistent with its unique fused anther locule. The divergence time of Aucuba was estimated to be approximately late Miocene. Extant Aucuba species derived from recent divergence events associated with the establishment of monsoonal climates in East Asia and climatic fluctuations.
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Affiliation(s)
- Yuan Huang
- School of Life Sciences, Yunnan Normal University, Kunming, China
- *Correspondence: Yuan Huang, ; Jiahui Chen,
| | - Linyuan Fan
- Yunnan General Administration of Foresty Seeds and Seedlings, Kunming, China
| | - Jian Huang
- Yunnan General Administration of Foresty Seeds and Seedlings, Kunming, China
| | - Guohua Zhou
- Chinese Medicinal Resources Co. LTD, Yunnan Baiyao Group, Kunming, China
| | - Xiong Chen
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Jiahui Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Yuan Huang, ; Jiahui Chen,
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12
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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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13
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Fu Q, Deng J, Chen M, Zhong Y, Lu GH, Wang YQ. Population genetic structure and connectivity of a riparian selfing herb Caulokaempferia coenobialis at a fine-scale geographic level in subtropical monsoon forest. BMC PLANT BIOLOGY 2021; 21:329. [PMID: 34238223 PMCID: PMC8265151 DOI: 10.1186/s12870-021-03101-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Rivers and streams facilitate movement of individuals and their genes across the landscape and are generally recognized as dispersal corridors for riparian plants. Nevertheless, some authors have reported directly contrasting results, which may be attributed to a complex mixture of factors, such as the mating system and dispersal mechanisms of propagules (seed and pollen), that make it difficult to predict the genetic diversity and population structure of riparian species. Here, we investigated a riparian self-fertilizing herb Caulokaempferia coenobialis, which does not use anemochory or zoochory for seed dispersal; such studies could contribute to an improved understanding of the effect of rivers or streams on population genetic diversity and structure in riparian plants. Using polymorphic ISSR and cpDNA loci, we studied the effect at a microgeographic scale of different stream systems (a linear stream, a dendritic stream, and complex transverse hydrological system) in subtropical monsoon forest on the genetic structure and connectivity of C. coenobialis populations across Dinghu Mountain (DH) and Nankun Mountain (NK). RESULTS The results indicate that the most recent haplotypes (DH: H7, H8; NK: h6, h7, h11, h12) are not shared among local populations of C. coenobialis within each stream system. Furthermore, downstream local populations do not accumulate genetic diversity, whether in the linear streamside local populations across DH (H: 0.091 vs 0.136) or the dendritic streamside local populations across NK (H: 0.079 vs 0.112, 0.110). Our results show that the connectivity of local C. coenobialis populations across DH and NK can be attributed to historical gene flows, resulting in a lack of spatial genetic structure, despite self-fertilization. Selfing C. coenobialis can maintain high genetic diversity (H = 0.251; I = 0.382) through genetic differentiation (GST = 0.5915; FST = 0.663), which is intensified by local adaptation and neutral mutation and/or genetic drift in local populations at a microgeographic scale. CONCLUSION We suggest that streams are not acting as corridors for dispersal of C. coenobialis, and conservation strategies for maintaining genetic diversity of selfing species should be focused on the protection of all habitat types, especially isolated fragments in ecosystem processes.
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Affiliation(s)
- Qiong Fu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yan Zhong
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guo-Hui Lu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ying-Qiang Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China.
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China.
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14
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Gu Y, Ma Q. The complete chloroplast genome of Pollia japonica (Commelinaceae) from Southeast China. Mitochondrial DNA B Resour 2021; 6:1486-1487. [PMID: 33969202 PMCID: PMC8078960 DOI: 10.1080/23802359.2021.1911717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 11/06/2022] Open
Abstract
The complete chloroplast genome of Pollia japonica, a medicinal herb native to East Asia was characterized. The size of the chloroplast genome is 165,076 bp in length with a large single copy (LSC) of 90,722 bp, a small single copy (SSC) of 19,146 bp, and a pair of inverted repeats of 27,604 bp. The chloroplast genome encodes a set of 131 genes, including 85 protein-coding, 38 tRNAs, and 8 rRNAs. Phylogenetic analysis based on complete chloroplast genomes validated the phylogenetic position of P. japonica and showed that the six species from Commelinales were fully resolved in a monophyletic clade sister to the Zingiberales. Species from the Zingiberales and Commelinales formed a molophyletic group sister to the Poales. The chloroplast genome of P. japonica provides an important resource for further study of molecular evolution in the Commelinaceae.
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Affiliation(s)
- Ye Gu
- Department of Gastroenterology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R.China
| | - Qing Ma
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, P.R.China
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15
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Yang Y, Zhou T, Qian Z, Zhao G. Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing. Genomics 2021; 113:1438-1447. [PMID: 33744343 DOI: 10.1016/j.ygeno.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 01/29/2023]
Abstract
China is a second center of oak diversity but with less intensively systematic studies. Here, with 49 species representing all four sections in China, we firstly gave insight into the comprehensive phylogenetic relationships of Chinese oaks based on 54 complete plastid genomes. Our results recovered a robust phylogenetic framework and provided strong support for most nodes. The phylogenetic tree supported Quercus section Ilex as not monophyletic, in which Quercus section Cyclobalanopsis and Quercus section Cerris were nested. Most likely, incomplete lineage sorting and/or introgression among ancestral lineages in these three sections resulted in this complex pattern. The current distribution, diversification and molecular differentiation of Q. sect. Ilex in China are likely consequences of local adaptation to the geographic and paleoclimatic changes, which were driven by the uplift of Tibetan Plateau, the Hengduan Mountains and the Himalayas.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China; School of Biological Science and Technology, Baotou Teachers' College, Baotou, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Zengqiang Qian
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China.
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16
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Zhu B, Qian F, Hou Y, Yang W, Cai M, Wu X. Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS One 2021; 16:e0248556. [PMID: 33711072 PMCID: PMC7954331 DOI: 10.1371/journal.pone.0248556] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 12/05/2022] Open
Abstract
Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.
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Affiliation(s)
- Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fang Qian
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yunfeng Hou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Weicheng Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mengxian Cai
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xiaoming Wu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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17
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Yang J, Takayama K, Youn JS, Pak JH, Kim SC. Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea. Genes (Basel) 2020; 11:E1338. [PMID: 33198274 PMCID: PMC7697516 DOI: 10.3390/genes11111338] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 01/18/2023] Open
Abstract
Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen-deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.
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Affiliation(s)
- JiYoung Yang
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Koji Takayama
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan;
| | - Jin-Suk Youn
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Jae-Hong Pak
- Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Gyeongsangbuk-do, Daegu 41566, Korea; (J.Y.); (J.-S.Y.)
| | - Seung-Chul Kim
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Gyeonggi-do, Suwon 16419, Korea
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19
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Shao L, Ning H. The complete chloroplast genome of Cymbidium serratum (Orchidaceae): a rare and Endangered species endemic to Southwest China. Mitochondrial DNA B Resour 2020; 5:2429-2431. [PMID: 33457815 PMCID: PMC7782322 DOI: 10.1080/23802359.2020.1775514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 11/01/2022] Open
Abstract
Cymbidium serratum is a dominant species in the large orchid family with beautiful flowers, thick petals, and long flowering periods, and has a long history of cultivation in Southwest China. However, its wild resources have been threatened with extinction due to environmental degradation and artificial exploitation. In this study, the complete chloroplast genome of C. serratum was obtained through Illumina sequencing. The size of chloroplast genome of C. serratum is 149,998 bp, including large single-copy (LSC) and small single-copy (SSC) regions over 84,854 bp and 13,926 bp, respectively, and two inverted repeats (IRs) of 25,609 bp. The total GC content was 37.11%. The chloroplast genome contains 129 genes, including 83 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The maximum-likelihood phylogenetic tree indicated that C. serratum is a sister species with the clade composed of C. faberi and C. goeringii. The complete chloroplast genome of C. serratum will contribute to protecting this highly endangered species, and provide genetic information about genetic diversity and sustainable use.
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Affiliation(s)
- Lei Shao
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Huijuan Ning
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
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20
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Sakulsathaporn A, Wonnapinij P, Suttangkakul A, Apisitwanich S, Vuttipongchaikij S. RNA editing in the chloroplast of Asian Palmyra palm (Borassus flabellifer). Genet Mol Biol 2020; 42:e20180371. [PMID: 31968044 PMCID: PMC7206934 DOI: 10.1590/1678-4685-gmb-2018-0371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 10/02/2019] [Indexed: 11/22/2022] Open
Abstract
We have identified 46 RNA editing sites located in 20 chloroplast (cp) genes of Borassus flabellifer (Asian Palmyra palm), family Arecaceae, and tested these genes for supporting phylogenetic study among the commelinids. Among the 46 sites, 43 sites were found to cause amino acid alterations, which were predicted to increase the hydrophobicity and transmembrane regions of the proteins, and one site was to cause a premature stop codon. Analysis of these editing sites with data obtained from seed plants showed that a number of shared-editing sites depend on the evolutionary relationship between plants. We reconstructed a deep phylogenetic relationship among the commelinids using seven RNA edited genes that are orthologous among monocots. This tree could represent the relationship among subfamilies of Arecaceae family, but was insufficient to represent the relationship among the orders of the commelinid. After adding eight gene sequences with high parsimony-informative characters (PICs), the tree topology was improved and could support the topology for the commelinid orders ((Arecales,Dasypogenaceae) (Zingiberales+Commelinales,Poales)). The result provides support for inherent RNA editing along the evolution of seed plants, and we provide an alternative set of loci for the phylogenetic tree reconstruction of Arecaceae's subfamilies.
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Affiliation(s)
- Arpakorn Sakulsathaporn
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- School of Natural Resource and Environmental Management,
Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai
Campus, Nong Khai 43000, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Somsak Apisitwanich
- Center for Agricultural Biotechnology, Kasetsart University,
Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
- Center of Excellence on Agricultural Biotechnology:
(AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart
University, 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900, Thailand
- Center of Advanced studies for Tropical Natural Resources,
Kasetsart University, Ngam Wong Wan, Chatuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health,
Kasetsart University (OmiKU), 50 Ngarm Wong Wan road, Chatuchak, Bangkok 10900,
Thailand
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Analysis of complete chloroplast genomes of Curcuma and the contribution to phylogeny and adaptive evolution. Gene 2020; 732:144355. [PMID: 31935501 DOI: 10.1016/j.gene.2020.144355] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/13/2023]
Abstract
Curcuma is an important member of Zingiberaceae. Many species of this genus are widely used in traditional medicine and have important cultural value in East Asia. Among them, C. longa is considered to be the main source of curcumin and has a very wide range of uses. The rapid development of molecular phylogeny has deepened our understanding of taxonomy and evolution of Curcuma. However, little is known about the chloroplast genome phylogeny and the genetic bases of adaptative evolution. In this work, we sequenced the complete chloroplast genome of 4 Curcuma species. Curcuma chloroplast genomes showed highly conserved structures and the length ranged from 159,423 bp to 152,723 bp. A total of 133 genes were observed. Multiple repeats and simple sequence repeats (SSRs) were detected. By comparing with related species, 7 highly variable regions were identified as potential specific DNA barcodes for species identification. Phylogenetic analysis of complete plastome sequences and specific data sets revealed discordance with expected genus boundary. Chloroplast phylogenetic relationships were better predicted by geography than by morphological and nuclear DNA, indicating a substantial existence of introgression. 9 genes were proved to have high posteriori probability in positive selection analysis, and 4 of them (psbA, psbD, PetA and rbcL) closely related to photosynthesis, implying that chloroplast genes may had undergone positive selection pressure in evolution. These results are of great significance for us to understand the genetic basis, phylogeny and adaptive evolution of Curcuma chloroplast.
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22
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Wei R, Zhang XC. Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis. Mol Phylogenet Evol 2019; 143:106699. [PMID: 31809851 DOI: 10.1016/j.ympev.2019.106699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 11/17/2022]
Abstract
Despite progress in resolving the phylogeny of twinsorus ferns (Diplazium) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related clades, suggesting a classic case of rapid evolutionary radiation. Here, we investigated the deep phylogenetic relationships within Diplazium by sampling all major clades and using 51 plastid genomes (plastomes), of which 38 were newly sequenced with high-throughput sequencing technology, resulting more than 127,000 informative sites. Using parsimony, maximum likelihood and Bayesian analyses of plastome sequences, we largely resolved the backbone of the phylogeny of Diplazium with strong support. However, we also detected phylogenetic incongruence among different datasets and moderately to poorly supported relationships, particularly at several extremely short internal branches. By using phylogenetic tree space and topology-clustering analyses, we provide evidence that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes, which may underlie the difficulty of systematics of Diplazium. Furthermore, our phylogenetic estimate offers more resolution over previous multilocus analyses, providing a framework for future taxonomic revisions of sectional classification of Diplazium. Our study demonstrates the advantage of a character-rich plastome dataset, combining the comparison of different phylogenetic methods, for resolving the recalcitrant lineages that have undergone rapid radiation and dramatic changes in evolutionary rates.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.
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23
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Kahraman K, Lucas SJ. Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. BMC Genomics 2019; 20:874. [PMID: 31747873 PMCID: PMC6865063 DOI: 10.1186/s12864-019-6253-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools. RESULTS Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. CONCLUSION In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.
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Affiliation(s)
- Kadriye Kahraman
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey.
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24
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Ma Q, Lu Y. The complete chloroplast genome of Eichhornia crassipes (Pontederiaceae) and phylogeny of commelinids. Mitochondrial DNA B Resour 2019; 4:3186-3187. [PMID: 33365911 PMCID: PMC7706893 DOI: 10.1080/23802359.2019.1667901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/16/2019] [Indexed: 11/04/2022] Open
Abstract
Eichhornia crassipes is a floating aquatic plant native to the American tropics. Here we reported and characterized the first complete chloroplast (cp) genome of Eichhornia crassipes and analyzed the phylogenomic relationship of Commelinids based on complete chloroplast sequences. The complete chloroplast genome of Eichhornia crassipes has a typical quadripartite structure with a total length of 161,783 bp. A total of 124 genes, including 85 encoding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes were annotated. The phylogenomic study validated the phylogenetic position of Eichhornia crassipes and showed that four species from Commelinales form a monophyletic group sister to Zingiberales.
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Affiliation(s)
- Qing Ma
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Yin Lu
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, Zhejiang, China
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25
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Ji Y, Liu C, Yang Z, Yang L, He Z, Wang H, Yang J, Yi T. Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in
Panax
(Araliaceae). Mol Ecol Resour 2019; 19:1333-1345. [DOI: 10.1111/1755-0998.13050] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Changkun Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Lifang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Kunming China
- School of Life Science Yunnan University Kunming China
| | - Zhengshan He
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
| | - Junbo Yang
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Tingshuang Yi
- Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming China
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Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China. FORESTS 2019. [DOI: 10.3390/f10070587] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.
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Khan A, Asaf S, Khan AL, Khan A, Al-Harrasi A, Al-Sudairy O, AbdulKareem NM, Al-Saady N, Al-Rawahi A. Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae. PeerJ 2019; 7:e7260. [PMID: 31328036 PMCID: PMC6625504 DOI: 10.7717/peerj.7260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 06/05/2019] [Indexed: 02/05/2023] Open
Abstract
Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study.
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Affiliation(s)
- Arif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Sajjad Asaf
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Adil Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Omar Al-Sudairy
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | | | | | - Ahmed Al-Rawahi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Gao B, Yuan L, Tang T, Hou J, Pan K, Wei N. The complete chloroplast genome sequence of Alpinia oxyphylla Miq. and comparison analysis within the Zingiberaceae family. PLoS One 2019; 14:e0218817. [PMID: 31233551 PMCID: PMC6590956 DOI: 10.1371/journal.pone.0218817] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
Alpinia oxyphylla Miq. (A. oxyphylla) is an important edible and traditional herbal medicine. In this study, the complete chloroplast genome of A. oxyphylla was sequenced, analysed, and compared to five species in the Zingiberaceae family. The size of the A. oxyphylla chloroplast genome was 161351 bp, which consisted of a large single-copy (LSC, 87248 bp) and small single-copy (SSC, 16175 bp) region separated by a pair of inverted repeats (IRa and IRb, 28964 bp each). The genome encoded 132 unique genes, including 87 protein-coding genes, 37 tRNAs and four rRNAs. The GC content of the genome was 36.17%. A total of 53 simple sequence repeats (SSRs) and 80 long repeats were identified in the A. oxyphylla chloroplast genome. The chloroplast genome of A. oxyphylla shared the highest sequence similarity of >90% with the chloroplast genome of A. zerumbet, and six chloroplast genomes in the Zingiberaceae family were compared by using CGView Comparison Tool (CCT). According to the phylogenetic tree, the Zingiberaceae family is divided into two categories, which coincide with the classification of the characteristics of sun-like and shade-like in plants. Our results reveal the phototrophic component of NADH-dehydrogenase (ndhB and ndhC), photosystem II (psbZ) and ATP synthase (atpE, atpF) exhibit adaptive evolution under different environments, and the strength of light is an important trigger for the adaptations at the chloroplast level.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Lin Yuan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Tianle Tang
- Environmental Science, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, China
| | - Jie Hou
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Kun Pan
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Na Wei
- Hainan Provincial Key Laboratory of R&D on Tropical Herbs, Hainan Medical University, Haikou, China
- School of Pharmacy, Hainan Medical University, Haikou, China
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29
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Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae). Mol Phylogenet Evol 2019; 135:1-11. [DOI: 10.1016/j.ympev.2019.02.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/27/2022]
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Zhou T, Ruhsam M, Wang J, Zhu H, Li W, Zhang X, Xu Y, Xu F, Wang X. The Complete Chloroplast Genome of Euphrasia regelii, Pseudogenization of ndh Genes and the Phylogenetic Relationships Within Orobanchaceae. Front Genet 2019; 10:444. [PMID: 31156705 PMCID: PMC6528182 DOI: 10.3389/fgene.2019.00444] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/29/2019] [Indexed: 12/31/2022] Open
Abstract
Euphrasia (Orobanchaceae) is a genus which is widely distributed in temperate regions of the southern and northern hemisphere. The taxonomy of Euphrasia is still controversial due to the similarity of morphological characters and a lack of genomic resources. Here, we present the first complete chloroplast (cp) genome of this taxonomically challenging genus. The cp genome of Euphrasia regelii consists of 153,026 bp, including a large single-copy region (83,893 bp), a small single-copy region (15,801 bp) and two inverted repeats (26,666 bp). There are 105 unique genes, including 71 protein-coding genes, 30 tRNA and 4 rRNA genes. Although the structure and gene order is comparable to the one in other angiosperm cp genomes, genes encoding the NAD(P)H dehydrogenase complex are widely pseudogenized due to mutations resulting in frameshifts, and stop codon positions. We detected 36 dispersed repeats, 7 tandem repeats and 65 simple sequence repeat loci in the E. regelii plastome. Comparative analyses indicated that the cp genome of E. regelii is more conserved compared to other hemiparasitic taxa in the Pedicularideae and Buchnereae. No structural rearrangements or loss of genes were detected. Our analyses suggested that three genes (clpP, ycf2 and rps14) were under positive selection and other genes under purifying selection. Phylogenetic analysis of monophyletic Orobanchaceae based on 45 plastomes indicated a close relationship between E. regelii and Neobartsia inaequalis. In addition, autotrophic lineages occupied the earliest diverging branches in our phylogeny, suggesting that autotrophy is the ancestral trait in this parasitic family.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Jian Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Honghong Zhu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Wenli Li
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), School of Life Sciences, Northwest University, Xi’an, China
| | - Yucan Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Fusheng Xu
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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Barrett CF, McKain MR, Sinn BT, Ge XJ, Zhang Y, Antonelli A, Bacon CD. Ancient Polyploidy and Genome Evolution in Palms. Genome Biol Evol 2019; 11:1501-1511. [PMID: 31028709 PMCID: PMC6535811 DOI: 10.1093/gbe/evz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Mechanisms of genome evolution are fundamental to our understanding of adaptation and the generation and maintenance of biodiversity, yet genome dynamics are still poorly characterized in many clades. Strong correlations between variation in genomic attributes and species diversity across the plant tree of life suggest that polyploidy or other mechanisms of genome size change confer selective advantages due to the introduction of genomic novelty. Palms (order Arecales, family Arecaceae) are diverse, widespread, and dominant in tropical ecosystems, yet little is known about genome evolution in this ecologically and economically important clade. Here, we take a phylogenetic comparative approach to investigate palm genome dynamics using genomic and transcriptomic data in combination with a recent, densely sampled, phylogenetic tree. We find conclusive evidence of a paleopolyploid event shared by the ancestor of palms but not with the sister clade, Dasypogonales. We find evidence of incremental chromosome number change in the palms as opposed to one of recurrent polyploidy. We find strong phylogenetic signal in chromosome number, but no signal in genome size, and further no correlation between the two when correcting for phylogenetic relationships. Palms thus add to a growing number of diverse, ecologically successful clades with evidence of whole-genome duplication, sister to a species-poor clade with no evidence of such an event. Disentangling the causes of genome size variation in palms moves us closer to understanding the genomic conditions facilitating adaptive radiation and ecological dominance in an evolutionarily successful, emblematic tropical clade.
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Affiliation(s)
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Yuqu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, PR China
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanical Gardens Kew, Richmond, United Kingdom
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
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Ma Q, Liang J. The first complete chloroplast genome of Pontederia cordata (Pontederiaceae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1553524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Qing Ma
- College of Biological and Environmental Engineering, Zhejiang Shuren University, Hangzhou, China
| | - Jiye Liang
- College of Plant Sciences, Tarim University, Alaer, China
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Liu C, Yang Z, Yang L, Yang J, Ji Y. The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae). PLANT DIVERSITY 2018; 40:265-276. [PMID: 30740573 PMCID: PMC6317490 DOI: 10.1016/j.pld.2018.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/03/2023]
Abstract
Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.
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Affiliation(s)
- Changkun Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhenyan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lifang Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- School of Life Science, Yunnan University, Kunming 650091, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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35
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Rosli R, Chan PL, Chan KL, Amiruddin N, Low ETL, Singh R, Harwood JL, Murphy DJ. In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:84-96. [PMID: 30107884 DOI: 10.1016/j.plantsci.2018.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/05/2018] [Accepted: 07/25/2018] [Indexed: 05/14/2023]
Abstract
The diacylglycerol acyltransferases (DGAT) (diacylglycerol:acyl-CoA acyltransferase, EC 2.3.1.20) are a key group of enzymes that catalyse the final and usually the most important rate-limiting step of triacylglycerol biosynthesis in plants and other organisms. Genes encoding four distinct functional families of DGAT enzymes have been characterised in the genome of the African oil palm, Elaeis guineensis. The contrasting features of the various isoforms within the four families of DGAT genes, namely DGAT1, DGAT2, DGAT3 and WS/DGAT are presented both in the oil palm itself and, for comparative purposes, in 12 other oil crop or model/related plants, namely Arabidopsis thaliana, Brachypodium distachyon, Brassica napus, Elaeis oleifera, Glycine max, Gossypium hirsutum, Helianthus annuus, Musa acuminata, Oryza sativa, Phoenix dactylifera, Sorghum bicolor, and Zea mays. The oil palm genome contains respectively three, two, two and two distinctly expressed functional copies of the DGAT1, DGAT2, DGAT3 and WS/DGAT genes. Phylogenetic analyses of the four DGAT families showed that the E. guineensis genes tend to cluster with sequences from P. dactylifera and M. acuminata rather than with other members of the Commelinid monocots group, such as the Poales which include the major cereal crops such as rice and maize. Comparison of the predicted DGAT protein sequences with other animal and plant DGATs was consistent with the E. guineensis DGAT1 being ER located with its active site facing the lumen while DGAT2, although also ER located, had a predicted cytosol-facing active site. In contrast, DGAT3 and some (but not all) WS/DGAT in E. guineensis are predicted to be soluble, cytosolic enzymes. Evaluation of E. guineensis DGAT gene expression in different tissues and developmental stages suggests that the four DGAT groups have distinctive physiological roles and are particularly prominent in developmental processes relating to reproduction, such as flowering, and in fruit/seed formation especially in the mesocarp and endosperm tissues.
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Affiliation(s)
- Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom; Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - John L Harwood
- School of Biosciences, University of Cardiff, Cardiff, CF10 3AX, United Kingdom
| | - Denis J Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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Yu X, Yang D, Guo C, Gao L. Plant phylogenomics based on genome-partitioning strategies: Progress and prospects. PLANT DIVERSITY 2018; 40:158-164. [PMID: 30740560 PMCID: PMC6137260 DOI: 10.1016/j.pld.2018.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 05/26/2023]
Abstract
The rapid expansion of next-generation sequencing (NGS) has generated a powerful array of approaches to address fundamental questions in biology. Several genome-partitioning strategies to sequence selected subsets of the genome have emerged in the fields of phylogenomics and evolutionary genomics. In this review, we summarize the applications, advantages and limitations of four NGS-based genome-partitioning approaches in plant phylogenomics: genome skimming, transcriptome sequencing (RNA-seq), restriction site associated DNA sequencing (RAD-Seq), and targeted capture (Hyb-seq). Of these four genome-partitioning approaches, targeted capture (especially Hyb-seq) shows the greatest promise for plant phylogenetics over the next few years. This review will aid researchers in their selection of appropriate genome-partitioning approaches to address questions of evolutionary scale, where we anticipate continued development and expansion of whole-genome sequencing strategies in the fields of plant phylogenomics and evolutionary biology research.
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Affiliation(s)
- Xiangqin Yu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Dan Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianming Gao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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37
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Li B, Zheng Y. Dynamic evolution and phylogenomic analysis of the chloroplast genome in Schisandraceae. Sci Rep 2018; 8:9285. [PMID: 29915292 PMCID: PMC6006245 DOI: 10.1038/s41598-018-27453-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022] Open
Abstract
Chloroplast genomes of plants are highly conserved in both gene order and gene content, are maternally inherited, and have a lower rate of evolution. Chloroplast genomes are considered to be good models for testing lineage-specific molecular evolution. In this study, we use Schisandraceae as an example to generate insights into the overall evolutionary dynamics in chloroplast genomes and to establish the phylogenetic relationship of Schisandraceae based on chloroplast genome data using phylogenomic analysis. By comparing three Schisandraceae chloroplast genomes, we demonstrate that the gene order, gene content, and length of chloroplast genomes in Schisandraceae are highly conserved but experience dynamic evolution among species. The number of repeat variations were detected, and the Schisandraceae chloroplast genome was revealed as unusual in having a 10 kb contraction of the IR due to the genome size variations compared with other angiosperms. Phylogenomic analysis based on 82 protein-coding genes from 66 plant taxa clearly elucidated that Schisandraceae is a sister to a clade that includes magnoliids, monocots, and eudicots within angiosperms. As to genus relationships within Schisandraceae, Kadsura and Schisandra formed a monophyletic clade which was sister to Illicium.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Chinese Academy of Forestry, Beijing, China.
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38
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Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG. Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. J Mol Evol 2018; 86:216-239. [PMID: 29556741 DOI: 10.1007/s00239-018-9837-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023]
Abstract
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.
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Affiliation(s)
- Erika Viljoen
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa.
| | - David J G Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Life and Consumer Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida, 1710, South Africa
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Yang Y, Zhu J, Feng L, Zhou T, Bai G, Yang J, Zhao G. Plastid Genome Comparative and Phylogenetic Analyses of the Key Genera in Fagaceae: Highlighting the Effect of Codon Composition Bias in Phylogenetic Inference. FRONTIERS IN PLANT SCIENCE 2018; 9:82. [PMID: 29449857 PMCID: PMC5800003 DOI: 10.3389/fpls.2018.00082] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/15/2018] [Indexed: 05/10/2023]
Abstract
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes (Fagus engleriana, Quercus spinosa, Quercus aquifolioides, and Quercus glauca) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference. The genomic analyses reveal that plastid genomes in Fagaceae are conserved. Comparing the phylogenetic relationships of the key genera in Fagaceae inferred from different codon positions and gene function datasets, we found that the first two codon sites dataset recovered nearly all relationships and received high support. Thus, the result suggested that codon composition bias had great influence on Fagaceae phylogenetic inference. Our study not only provides basic understanding of Fagaceae plastid genomes, but also illuminates the effectiveness of plastid phylogenomics in resolving relationships of this intractable family.
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Affiliation(s)
- Yanci Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Juan Zhu
- Middle School of Xi'an Electronic Science and Technology, Xi'an, China
| | - Li Feng
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
| | - Guoqing Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, China
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40
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Sakulsathaporn A, Wonnapinij P, Vuttipongchaikij S, Apisitwanich S. The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer). BMC Res Notes 2017; 10:740. [PMID: 29246263 PMCID: PMC5732391 DOI: 10.1186/s13104-017-3077-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 12/08/2017] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE Borassus flabellifer or Asian Palmyra palm is widely distributed in South and Southeast Asia and is horticultural and economic importance for its fruit and palm sugar production. However, its population is in rapid decline, and only a few genetic data are available. We sequenced the complete chloroplast (cp) genome of B. flabellifer to provide its genetic data for further utilization. RESULTS The cp genome was obtained by Illumina sequencing and manual gap fillings providing 160,021 bp in length containing a pair of inverted repeats (IRs) with 27,256 bp. These IRs divide the genome into a large single copy region 87,444 bp and a small single copy region 18,065 bp. In total, 113 unique genes, 134 SSRs and 47 large repeats were identified. This is the first complete cp genome reported in the genus Borassus. A comparative analysis among members of the Borasseae tribe revealed that the B. flabellifer cp genome is, so far, the largest and the cp genomes of this tribe have a similar structure, gene number and gene arrangement. A phylogenetic tree reconstructed based on 74 protein-coding genes from 70 monocots demonstrates short branch lengths indicating slow evolutionary rates of cp genomes in family Arecaceae.
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Affiliation(s)
- Arpakorn Sakulsathaporn
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140 Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chattuchak, Bangkok, 10900 Thailand
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chattuchak, Bangkok, 10900 Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
| | - Somsak Apisitwanich
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140 Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
- Center of Advanced Studies for Tropical Natural Resources, Kasetsart University, 50 Ngam Wong Wan, Chattuchak, Bangkok, 10900 Thailand
- Special Research Unit in Microalgal Molecular Genetics and Functional Genomics (MMGFG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngarm Wong Wan Road, Chattuchak, Bangkok, 10900 Thailand
- School of Science, Mae Fah Luang University, Chiang-Rai, 57100 Thailand
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Léveillé-Bourret É, Starr JR, Ford BA. Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae). Mol Phylogenet Evol 2017; 119:93-104. [PMID: 29113924 DOI: 10.1016/j.ympev.2017.10.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 10/18/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the world's most diverse plant lineages.
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Affiliation(s)
| | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Bruce A Ford
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Poczai P, Hyvönen J. The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis. PLoS One 2017; 12:e0187199. [PMID: 29095905 PMCID: PMC5667773 DOI: 10.1371/journal.pone.0187199] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 10/16/2017] [Indexed: 11/24/2022] Open
Abstract
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales. The plastome of Spanish moss has a quadripartite structure consisting of a large single copy (LSC, 87,439 bp), two inverted regions (IRa and IRb, 26,803 bp) and short single copy (SSC, 18,612 bp) region. The plastid genome had 37.2% GC content and 134 genes with 88 being unique protein-coding genes and 20 of these are duplicated in the IR, similar to other reported bromeliads. Our study shows that early diverging lineages of Poales do not have high substitution rates as compared to grasses, and plastid genomes of bromeliads show structural features considered to be ancestral in graminids. These include the loss of the introns in the clpP and rpoC1 genes and the complete loss or partial degradation of accD and ycf genes in the Graminid clade. Further structural rearrangements appeared in the graminids lacking in Spanish moss, which include a 28-kb inversion between the trnG-UCC-rps14 region and 6-kb in the trnG-UCC-psbD, followed by a third <1kb inversion in the trnT sequence.
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Affiliation(s)
- Péter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Jaakko Hyvönen
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
- Dept. Biosci. (Plant Biology), University of Helsinki, Helsinki, Finland
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Yang Z, Ji Y. Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. FRONTIERS IN PLANT SCIENCE 2017; 8:1536. [PMID: 28955348 PMCID: PMC5601906 DOI: 10.3389/fpls.2017.01536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/22/2017] [Indexed: 05/08/2023]
Abstract
The Arcto-Tertiary relict genera, Camptotheca, Davidia, and Nyssa represent deep lineages in the asterid order Cornales. Recent phylogenetic studies suggested that these genera should be placed in a newly circumscribed family, Nyssaceae. However, because these analyses were based upon a few genes, it is prudent and necessary to examine further evidence before adopting this taxonomic treatment. In this study, we determined the complete chloroplast (cp) genomes of Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Their cp genomes ranged from 156,672 to 158,409 bp, which included 115 genes, and their genome features were highly similar to those of other species within the order Cornales. The phylogenetic relationships among the genera Camptotheca, Davidia, Nyssa, and 23 related taxa in the asterids were analyzed based on 73 protein-coding genes from the cp genomes. All of the previously recognized major clades (namely Cornales, Ericales, Campanulids, and Lamiids) in the asterids, as well as their relationships, were recovered with robust support. A clade including the genera Davidia, Nyssa, Camptotheca, and Diplopanax, was resolved as a well-supported monophyletic group, which was fully separated from the family Cornaceae by the family Hydrangeaceae. Our results provide novel evidence to support the acceptance of the family Nyssaceae outlined by the updated Angiosperm Phylogeny Group.
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Affiliation(s)
| | - Yunheng Ji
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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44
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Izan S, Esselink D, Visser RGF, Smulders MJM, Borm T. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences. FRONTIERS IN PLANT SCIENCE 2017; 8:1271. [PMID: 28824658 PMCID: PMC5539191 DOI: 10.3389/fpls.2017.01271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 07/05/2017] [Indexed: 05/11/2023]
Abstract
Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb), Aegilops tauschii (4 Gb) and Paphiopedilum henryanum (25 Gb). We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.
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Affiliation(s)
- Shairul Izan
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Danny Esselink
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
| | | | | | - Theo Borm
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
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45
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Lin CS, Chen JJW, Chiu CC, Hsiao HCW, Yang CJ, Jin XH, Leebens-Mack J, de Pamphilis CW, Huang YT, Yang LH, Chang WJ, Kui L, Wong GKS, Hu JM, Wang W, Shih MC. Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:994-1006. [PMID: 28258650 DOI: 10.1111/tpj.13525] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/20/2017] [Accepted: 02/23/2017] [Indexed: 05/23/2023]
Abstract
The chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of about 30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and Dendrobium catenatum, most of the 11 chloroplast genome-encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genome. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost, resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for P. equestris, D. officinale and D. catenatum, which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid-encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.
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Affiliation(s)
- Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Han C W Hsiao
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, Taiwan
| | - Chen-Jui Yang
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Xiao-Hua Jin
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | | | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ling-Hung Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jer-Ming Hu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Wen Wang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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Do HDK, Kim JH. A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae. FRONTIERS IN PLANT SCIENCE 2017; 8:693. [PMID: 28588587 PMCID: PMC5438981 DOI: 10.3389/fpls.2017.00693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/18/2017] [Indexed: 05/27/2023]
Abstract
Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections (Veratrum and Fuscoveratrum) of Veratrum. Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3. Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.
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Affiliation(s)
| | - Joo-Hwan Kim
- Plant Systematics Laboratory, Department of Biological Science, Gachon UniversitySeongnam, South Korea
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47
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Léveillé-Bourret É, Starr JR, Ford BA, Moriarty Lemmon E, Lemmon AR. Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics. Syst Biol 2017; 67:94-112. [DOI: 10.1093/sysbio/syx050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/28/2017] [Indexed: 11/13/2022] Open
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48
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Yang J, Yue M, Niu C, Ma XF, Li ZH. Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium. Genes (Basel) 2017; 8:E124. [PMID: 28422071 PMCID: PMC5406871 DOI: 10.3390/genes8040124] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/01/2017] [Accepted: 04/05/2017] [Indexed: 12/14/2022] Open
Abstract
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing. We investigated the gene organization, order, size and repeat sequences of the cp genome and constructed the phylogenetic relationships of Notopterygium species based on the chloroplast DNA and nuclear internal transcribed spacer (ITS) sequences. Comparative analysis of plastid genome showed that the cp DNA are the standard double-stranded molecule, ranging from 157,462 bp (N. oviforme) to 159,607 bp (N. forrestii) in length. The circular DNA each contained a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs). The cp DNA of four species contained 85 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes, respectively. We determined the marked conservation of gene content and sequence evolutionary rate in the cp genome of four Notopterygium species. Three genes (psaI, psbI and rpoA) were possibly under positive selection among the four sampled species. Phylogenetic analysis showed that four Notopterygium species formed a monophyletic clade with high bootstrap support. However, the inconsistent interspecific relationships with the genus Notopterygium were identified between the cp DNA and ITS markers. The incomplete lineage sorting, convergence evolution or hybridization, gene infiltration and different sampling strategies among species may have caused the incongruence between the nuclear and cp DNA relationships. The present results suggested that Notopterygium species may have experienced a complex evolutionary history and speciation process.
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Affiliation(s)
- Jiao Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Chuan Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
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Li P, Lu RS, Xu WQ, Ohi-Toma T, Cai MQ, Qiu YX, Cameron KM, Fu CX. Comparative Genomics and Phylogenomics of East Asian Tulips ( Amana, Liliaceae). FRONTIERS IN PLANT SCIENCE 2017; 8:451. [PMID: 28421090 PMCID: PMC5378804 DOI: 10.3389/fpls.2017.00451] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 03/15/2017] [Indexed: 05/09/2023]
Abstract
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions. Each cp genome equivalently contains 112 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 78 protein coding genes. Gene content, gene order, AT content, and IR/SC boundary structure are nearly identical among all Amana cp genomes. However, the relative contraction and expansion of the IR/SC borders among the six Amana cp genomes results in length variation among them. Simple sequence repeat (SSR) analyses of these Amana cp genomes indicate that the richest SSRs are A/T mononucleotides. The number of repeats among the six Amana species varies from 54 (A. anhuiensis) to 69 (Amana kuocangshanica) with palindromic (28-35) and forward repeats (23-30) as the most common types. Phylogenomic analyses based on these complete cp genomes and 74 common protein-coding genes strongly support the monophyly of the genus, and a sister relationship between Amana and Erythronium, rather than a shared common ancestor with Tulipa. Nine DNA markers (rps15-ycf1, accD-psaI, petA-psbJ, rpl32-trnL, atpH-atpI, petD-rpoA, trnS-trnG, psbM-trnD, and ycf4-cemA) with number of variable sites greater than 0.9% were identified, and these may be useful for future population genetic and phylogeographic studies of Amana species.
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Affiliation(s)
- Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Rui-Sen Lu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Wu-Qin Xu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Tetsuo Ohi-Toma
- Botanical Gardens, Graduate School of Science, University of TokyoTokyo, Japan
| | - Min-Qi Cai
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | | | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang UniversityHangzhou, China
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50
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Fisher AE, Hasenstab KM, Bell HL, Blaine E, Ingram AL, Columbus JT. Evolutionary history of chloridoid grasses estimated from 122 nuclear loci. Mol Phylogenet Evol 2016; 105:1-14. [DOI: 10.1016/j.ympev.2016.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 10/25/2022]
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