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Ping J, Hao J, Wang T, Su Y. Comparative analysis of plastid genomes reveals rearrangements, repetitive sequence features, and phylogeny in the Annonaceae. Front Plant Sci 2024; 15:1351388. [PMID: 38693922 PMCID: PMC11061511 DOI: 10.3389/fpls.2024.1351388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
The Annonaceae stands as the most species rich family in the Magnoliales, a basal group of angiosperms. Widely distributed in tropical and subtropical regions, it holds significant ecological and economic value. The plastid genome (plastome) is often employed in studies related to plant phylogenetics, comparative genomics, evolutionary biology, and genetic engineering. Nonetheless, research progress on plastid genomics in the Annonaceae has been relatively slow. In this study, we analyzed the structure and repetitive sequence features of plastomes from 28 Annonaceae species. Among them, Mitrephora tomentosa and Desmos chinensis were newly sequenced, with sizes of 160,157 bp and 192,167 bp, and GC contents of 38.3% and 38.4%, respectively. The plastome size in the Annonaceae ranged from 158,837 bp to 202,703 bp, with inverted repeat (IR) region sizes ranging from 64,621 bp to 25,861 bp. Species exhibiting expansion in the IR region showed an increase in plastome size and gene number, frequent boundary changes, different expansion modes (bidirectional or unidirectional), and an increase in repetitive sequences. Specifically, a large number of dispersed repetitive sequences lead to an increase in the size of the LSC region in Goniothalamus tamirensis. Phylogenetic analysis revealed Annonoideae and Malmeoideae as monophyletic groups and sister clades, with Cananga odorata outside of them, followed by Anaxagorea javanica. This research uncovers the structural variation characteristics of plastomes in the Annonaceae, providing valuable information for understanding the phylogeny and plastome evolution of Annonaceae.
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Affiliation(s)
- Jingyao Ping
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jing Hao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Research Institute of Sun Yat-Sen University, Shenzhen, China
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Wang X, Liao S, Zhang Z, Zhang J, Mei L, Li H. Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae). Front Plant Sci 2024; 15:1354812. [PMID: 38595762 PMCID: PMC11002808 DOI: 10.3389/fpls.2024.1354812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024]
Abstract
The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.
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Affiliation(s)
- Xiaomei Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuai Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Zhen Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - Jianhang Zhang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, China
| | - Li Mei
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hongqing Li
- School of Life Sciences, East China Normal University, Shanghai, China
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Cao J, Wang H, Cao Y, Kan S, Li J, Liu Y. Extreme Reconfiguration of Plastid Genomes in Papaveraceae: Rearrangements, Gene Loss, Pseudogenization, IR Expansion, and Repeats. Int J Mol Sci 2024; 25:2278. [PMID: 38396955 PMCID: PMC10888665 DOI: 10.3390/ijms25042278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the complete plastomes from twenty-two species, covering seventeen genera from three subfamilies (Fumarioideae, Hypecooideae, and Papaveroideae) of Papaveraceae. Our results revealed a high level of variability in the plastid genome size of Papaveraceae, ranging from 151,864 bp to 219,144 bp in length, which might be triggered by the expansion of the IR region and a large number of repeat sequences. Moreover, we detected numerous large-scale rearrangements, primarily occurring in the plastomes of Fumarioideae and Hypecooideae. Frequent gene loss or pseudogenization were also observed for ndhs, accD, clpP, infA, rpl2, rpl20, rpl32, rps16, and several tRNA genes, particularly in Fumarioideae and Hypecooideae, which might be associated with the structural variation in their plastomes. Furthermore, we found that the plastomes of Fumarioideae exhibited a higher GC content and more repeat sequences than those of Papaveroideae. Our results showed that Papaveroideae generally displayed a relatively conserved plastome, with the exception of Eomecon chionantha, while Fumarioideae and Hypecooideae typically harbored highly reconfigurable plastomes, showing high variability in the genome size, gene content, and gene order. This study provides insights into the plastome evolution of Papaveraceae and may contribute to the development of effective molecular markers.
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Affiliation(s)
- Jialiang Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Hongwei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Yanan Cao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
| | - Shenglong Kan
- Marine College, Shandong University, Weihai 264209, China;
| | - Jiamei Li
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanyan Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (J.C.); (H.W.); (Y.C.)
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Wu D, Qin Q, Wang X, Niu Y, Zhang S, Mu Z. Sequence Analysis of the Plastomes of Two Tibetan Medicinal Plants of the Family Papaveraceae. FRONT BIOSCI-LANDMRK 2023; 28:352. [PMID: 38179751 DOI: 10.31083/j.fbl2812352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/12/2023] [Accepted: 09/05/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND With the rapid development of next-generation sequencing technology, more plants plastomes have been sequenced, further advancing species identification and phylogenetic studies. However, there are a few studies on the genetic and phylogenetic analysis of the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms. METHODS In this study, we sequenced and analyzed the plastomes of Dicranostigma lactucoides Hook. f. et Thoms. and Hypecoum leptocarpum Hook. f. et Thoms., and conducted a phylogenetic analysis using 13 related species. RESULTS The results showed that the plastomes of both D. lactucoides and H. leptocarpum had a typical tetrad structure, with sizes of 166,819 bp and 163,282 bp, respectively. We annotated 133 genes for D. lactucoides and 120 genes for H. leptocarpum. A total of 72 and 43 simple repetitive sequences were detected in D. lactucoides and H. leptocarpum, respectively. Codon preference analysis showed that the relative usage frequency of codons and the relative abundance of synonymous codons used were the same for both plastomes. Nucleotide polymorphism analysis identified seven variant loci with high nucleotide diversity (Pi) values, all located in the large single copy (LSC) region. Inverted repeat (IR) boundary analysis revealed differences in gene types and locations on both sides of the boundary, except for the small single copy/inverted repeat a (SSC/IRa) boundary. The phylogenetic analysis showed the species clustered into two major groups, one with five genera (Hypecoum, Corydalis, Papaver, Meconopsis, and Dicranostigma) and the other with two genera (Coreanomecon; and Hylomecon). CONCLUSIONS Comparative analysis of the plastome genomic characteristics and phylogeny of D. lactucoides and H. leptocarpum laid the foundation for identifying the above two species and the phylogenetic study and comprehensive exploitation of the Papaveraceae.
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Affiliation(s)
- Danyang Wu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Qian Qin
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Xiaoyun Wang
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Yiming Niu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Shouwen Zhang
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
| | - Zejing Mu
- The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China
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Wang J, Liao X, Li Y, Ye Y, Xing G, Kan S, Nie L, Li S, Tembrock LR, Wu Z. Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars. Genes (Basel) 2023; 14:1743. [PMID: 37761883 PMCID: PMC10531169 DOI: 10.3390/genes14091743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/20/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources.
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Affiliation(s)
- Jie Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Yongyao Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Yuanjun Ye
- Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China;
| | - Guoming Xing
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (J.W.); (G.X.); (S.L.)
| | - Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (X.L.); (Y.L.); (S.K.); (L.N.)
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Li CJ, Xie XT, Liu HX, Wang RN, Li DZ. Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses. Front Plant Sci 2023; 14:1144406. [PMID: 37063184 PMCID: PMC10102522 DOI: 10.3389/fpls.2023.1144406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Lobelia species, as rich source of the alkaloid lobeline which has been shown to have important biological activity, have been used in folk medicine throughout East Asia to treat various diseases. However, Lobelia is a complex and varied genus in East Asia and is thus difficult to identify. Genomic resources would aid identification, however the availability of such information is poor, preventing a clear understanding of their evolutionary history from being established. To close this gap in the available genomic data, in this study, 17 plastomes of East Asian lobelias were newly sequenced and assembled. Although the plastomes of Lobelia sect. Hypsela, L. sect. Speirema, and L. sect. Rhynchopetalum shared the gene structure, the inverted repeat (IR)/large single copy (LSC) boundaries, genome size, and the number of repeats were variable, indicating the non-conservative nature of plastome evolution within these sections. However, the genomes of the Lobelia sect. Delostemon and L. sect. Stenotium showed rearrangements, revealing that these two sections might have undergone different evolutionary histories. We assessed nine hotspot genes and 27-51 simple sequence repeat motifs, which will also serve as valuable DNA barcode regions in future population genetics studies and for the delineation of plant species. Our phylogenetic analysis resolved the evolutionary positions of the five sections in agreement with previous evolutionary trees based on morphological features. Although phylogenetic reconstruction of Lobelioideae based on the rpoC2 gene has rarely been performed, our results indicated that it contains a considerable amount of phylogenetic information and offers great promise for further phylogenetic analysis of Lobelioideae. Our site-specific model identified 173 sites under highly positive selections. The branch-site model exhibited 11 positive selection sites involving four genes in the East Asian branches. These four genes may play critical roles in the adaptation of East Asian taxa to diverse environments. Our study is the first to detect plastome organization, phylogenetic utility, and signatures of positive selection in the plastomes of East Asian lobelias, which will help to further advance taxonomic and evolutionary studies and the utilization of medicinal plant resources.
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Affiliation(s)
- Chun-Jiao Li
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xin-Tong Xie
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
| | - Hong-Xin Liu
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning, China
| | - Ruo-Nan Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Kim YK, Cheon SH, Hong JR, Kim KJ. Evolutionary Patterns of the Chloroplast Genome in Vanilloid Orchids (Vanilloideae, Orchidaceae). Int J Mol Sci 2023; 24. [PMID: 36835219 DOI: 10.3390/ijms24043808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
The Vanilloideae (vanilloids) is one of five subfamilies of Orchidaceae and is composed of fourteen genera and approximately 245 species. In this study, the six new chloroplast genomes (plastomes) of vanilloids (two Lecanorchis, two Pogonia, and two Vanilla species) were decoded, and then the evolutionary patterns of plastomes were compared to all available vanilloid plastomes. Pogonia japonica has the longest plastome, with 158,200 bp in genome size. In contrast, Lecanorchis japonica has the shortest plastome with 70,498 bp in genome size. The vanilloid plastomes have regular quadripartite structures, but the small single copy (SSC) region was drastically reduced. Two different tribes of Vanilloideae (Pogonieae and Vanilleae) showed different levels of SSC reductions. In addition, various gene losses were observed among the vanilloid plastomes. The photosynthetic vanilloids (Pogonia and Vanilla) showed signs of stage 1 degradation and had lost most of their ndh genes. The other three species (one Cyrotsia and two Lecanorchis), however, had stage 3 or stage 4 degradation and had lost almost all the genes in their plastomes, except for some housekeeping genes. The Vanilloideae were located between the Apostasioideae and Cypripedioideae in the maximum likelihood tree. A total of ten rearrangements were found among ten Vanilloideae plastomes when compared to the basal Apostasioideae plastomes. The four sub-regions of the single copy (SC) region shifted into an inverted repeat (IR) region, and the other four sub-regions of the IR region shifted into the SC regions. Both the synonymous (dS) and nonsynonymous (dN) substitution rates of IR in-cooperated SC sub-regions were decelerated, while the substitution rates of SC in-cooperated IR sub-regions were accelerated. A total of 20 protein-coding genes remained in mycoheterotrophic vanilloids. Almost all these protein genes show accelerated base substitution rates compared to the photosynthetic vanilloids. Two of the twenty genes in the mycoheterotrophic species faced strong "relaxed selection" pressure (p-value < 0.05).
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Zecca G, Panzeri D, Grassi F. Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous-Palaeogene (K/Pg) transition. Ann Bot 2022; 130:965-980. [PMID: 36282948 PMCID: PMC9851337 DOI: 10.1093/aob/mcac128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Although plastid genes are widely used in phylogenetic studies, signals of positive selection have been scarcely investigated in the grape family. The plastomes from 91 accessions of Vitaceae were examined to understand the extent to which positive selection is present and to identify which genes are involved. Moreover, the changes through time of genes under episodic positive selection were investigated and the hypothesis of an adaptive process following the Cretaceous-Palaeogene (K/Pg) transition about 66 million years ago was tested. METHODS Different codon-substitution models were used to assess pervasive and episodic positive selection events on 70 candidate plastid genes. Divergence times between lineages were estimated and stochastic character mapping analysis was used to simulate variation over time of the genes found to be under episodic positive selection. KEY RESULTS A total of 20 plastid genes (29 %) showed positive selection. Among them, 14 genes showed pervasive signatures of positive selection and nine genes showed episodic signatures of positive selection. In particular, four of the nine genes (psbK, rpl20, rpoB, rps11) exhibited a similar pattern showing an increase in the rate of variation close to the K/Pg transition. CONCLUSION Multiple analyses have shown that the grape family has experienced ancient and recent positive selection events and that the targeted genes are involved in essential functions such as photosynthesis, self-replication and metabolism. Our results are consistent with the idea that the K/Pg transition has favoured an increased rate of change in some genes. Intense environmental perturbations have influenced the rapid diversification of certain lineages, and new mutations arising on some plastid genes may have been fixed by natural selection over the course of many generations.
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Affiliation(s)
- Giovanni Zecca
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Davide Panzeri
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
| | - Fabrizio Grassi
- University of Milan-Bicocca, Department of Biotechnology and Bioscience, Piazza della Scienza 2, 20126, Milano, Italy
- NBFC, National Biodiversity Future Center, Palermo 90133, Italy
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Zhang H, Zhang X, Sun Y, Landis JB, Li L, Hu G, Sun J, Tiamiyu BB, Kuang T, Deng T, Sun H, Wang H. Plastome phylogenomics and biogeography of the subfam. Polygonoideae (Polygonaceae). Front Plant Sci 2022; 13:893201. [PMID: 36275552 PMCID: PMC9581148 DOI: 10.3389/fpls.2022.893201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Polygonaceae has a complex taxonomic history, although a few studies using plastid or nuclear DNA fragments have explored relationships within this family, intrafamilial relationships remain controversial. Here, we newly sequenced and annotated 17 plastomes representing 12 genera within Polygonaceae. Combined with previously published data, a total of 49 plastomes representing 22/46 Polygonaceae genera and 16/20 Polygonoideae genera were collected to infer the phylogeny of Polygonaceae, with an emphasis on Polygonoideae. Plastome comparisons revealed high conservation within Polygonoideae in structure and gene order. Phylogenetic analyses using both Maximum Likelihood and Bayesian methods revealed two major clades and seven tribes within Polygonoideae. BEAST and S-DIVA analyses suggested a Paleocene origin of Polygonoideae in Asia. While most genera of Polygonoideae originated and further diversified in Asia, a few genera experienced multiple long-distance dispersal events from Eurasia to North America after the Miocene, with a few dispersal events to the Southern Hemisphere also being detected. Both ancient vicariance and long-distance events have played important roles in shaping the current distribution pattern of Polygonoideae.
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Affiliation(s)
- Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jacob B. Landis
- Section of Plant Biology and the L.H. Bailey Hortorium, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Jiao Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bashir B. Tiamiyu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianhui Kuang
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Tao Deng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, 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
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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10
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Gagnon E, Hilgenhof R, Orejuela A, McDonnell A, Sablok G, Aubriot X, Giacomin L, Gouvêa Y, Bragionis T, Stehmann JR, Bohs L, Dodsworth S, Martine C, Poczai P, Knapp S, Särkinen T. Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum. Am J Bot 2022; 109:580-601. [PMID: 35170754 PMCID: PMC9321964 DOI: 10.1002/ajb2.1827] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/14/2021] [Indexed: 05/13/2023]
Abstract
PREMISE Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants. METHODS A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) and nine regions (ITS, waxy, and seven plastid markers). The robustness of this topology is tested by examining a full plastome dataset with 140 species and a nuclear target-capture dataset with 39 species of Solanum (Angiosperms353 probe set). RESULTS While the taxonomic framework of Solanum remained stable, gene tree conflicts and discordance between phylogenetic trees generated from the target-capture and plastome datasets were observed. The latter correspond to regions with short internodal branches, and network analysis and polytomy tests suggest the backbone is composed of three polytomies found at different evolutionary depths. The strongest area of discordance, near the crown node of Solanum, could potentially represent a hard polytomy. CONCLUSIONS We argue that incomplete lineage sorting due to rapid diversification is the most likely cause for these polytomies, and that embracing the uncertainty that underlies them is crucial to understand the evolution of large and rapidly radiating lineages.
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Affiliation(s)
- Edeline Gagnon
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Rebecca Hilgenhof
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RoadEdinburghEH9 3JHUK
| | - Angela McDonnell
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden, 1000 Lake Cook RdGlencoeIllinois60022USA
| | - Gaurav Sablok
- Finnish Museum of Natural History (Botany Unit)University of HelsinkiPO Box 7 FI‐00014HelsinkiFinland
- Organismal and Evolutionary Biology Research Programme (OEB)Viikki Plant Science Centre (ViPS)PO Box 65, FI‐00014 University of HelsinkiFinland
| | - Xavier Aubriot
- Université Paris‐Saclay, CNRS, AgroParisTech, ÉcologieSystématique et ÉvolutionOrsay91405France
| | - Leandro Giacomin
- Instituto de Ciências e Tecnologia das Águas & Herbário HSTMUniversidade Federal do Oeste do Pará, Rua Vera Paz, sn, Santarém, CEP 68040‐255PABrazil
| | - Yuri Gouvêa
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - Thamyris Bragionis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - João Renato Stehmann
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais—UFMGAv. Antônio Carlos, 6627, Pampulha, Belo Horizonte, CEP 31270‐901MGBrazil
| | - Lynn Bohs
- Department of BiologyUniversity of UtahSalt Lake CityUtah84112USA
| | - Steven Dodsworth
- School of Life SciencesUniversity of Bedfordshire, University SquareLutonLU1 3JUUK
- Royal Botanic Gardens, Kew, RichmondSurreyTW9 3AEUK
| | | | - Péter Poczai
- Finnish Museum of Natural History (Botany Unit)University of HelsinkiPO Box 7 FI‐00014HelsinkiFinland
- Faculity of Environmental and Biological SciencesUniversity of HelsinkiFI‐00014Finland
| | - Sandra Knapp
- Department of Life SciencesNatural History MuseumCromwell RoadLondonSW7 5BDUK
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
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11
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Zhang J, Wang Y, Chen T, Chen Q, Wang L, Liu ZS, Wang H, Xie R, He W, Li M, Liu CL, Yang SF, Li MY, Lin YX, Zhang YT, Zhang Y, Luo Y, Tang HR, Gao LZ, Wang XR. Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry. Front Plant Sci 2021; 12:736053. [PMID: 34868119 PMCID: PMC8639594 DOI: 10.3389/fpls.2021.736053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including Cerasus (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Tao Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhen-shan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Rui Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Cong-li Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shao-feng Yang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Meng-yao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yuan-xiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yun-ting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Hao-ru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Li-zhi Gao
- Institute of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-rong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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12
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Pérez‐Pérez MA, Yu W. Pleistocene origin and colonization history of Lobelia columnaris Hook. f. (Campanulaceae: Lobelioideae) across sky islands of West Central Africa. Ecol Evol 2021; 11:15860-15873. [PMID: 34824795 PMCID: PMC8601881 DOI: 10.1002/ece3.8256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 11/08/2022] Open
Abstract
We aimed to infer ancestral area and historical colonization of Lobelia columnaris in the sky islands of Bioko and Cameroon through dated phylogeny using chloroplast genomes. Specifically, we aim to answer the following questions: (1) What are the phylogenetic relationships among Bioko Island and Cameroon populations? (2) Are the older populations found in the older sky islands? We assembled novel plastomes from 20 individuals of L. columnaris from 5 mountain systems. The plastome data were explored with phylogenetic analyses using Maximum Likelihood and Bayesian Inference. The populations of L. columnaris have a monophyletic origin, subdivided into three plastomes-geographic clades. The plastid phylogenomic results and age of the sky islands indicate that L. columnaris colonized first along with the Cameroon Volcanic Line's young sky islands of Bioko. The crown group (1.54 Ma) split the population in Bioko and mainland Cameroon. It is possible that Bioko was the ancestral area and likely isolated during cold and dry conditions in forest refugia. Presumably, the colonization history occurred during the middle-late Pleistocene from South Bioko's young sky island to North Bioko and the northern old sky islands in Cameroon. Furthermore, the central depression with lowland forest between North and South Bioko is a current geographic barrier that keeps separating the populations of Bioko from each other. Also, the shallow sea channel keeps isolated the populations of Bioko and the mainland populations. The Pleistocene climatic oscillations led to the divergence of the Cameroon and Bioko populations into three clades. L. columnaris colonized the older sky islands in mainland Cameroon after establishment in Bioko's younger sky islands. Contrary to expectations, the biogeography history was an inverse progression with respect to the age of the Afromontane sky islands.
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Affiliation(s)
- Miguel A. Pérez‐Pérez
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
- Department of Biodiversity, Earth & Environmental ScienceDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Wen‐Bin Yu
- Center for Integrative ConservationXishuangbanna Tropical Botanical GardenMenglaChina
- Center of Conservation Biology, Core Botanical GardensChinese Academy of SciencesMenglaChina
- Southeast Asia Biodiversity Research InstituteChinese Academy of ScienceYezinMyanmar
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13
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. Am J Bot 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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14
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Cvetković T, Areces-Berazain F, Hinsinger DD, Thomas DC, Wieringa JJ, Ganesan SK, Strijk JS. Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l. G3 (Bethesda) 2021; 11:6248091. [PMID: 33892500 PMCID: PMC8496235 DOI: 10.1093/g3journal/jkab136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/11/2021] [Indexed: 11/22/2022]
Abstract
Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage /Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into /Byttneriina (/Grewioideae +/Byttnerioideae) and /Malvadendrina. Within /Malvadendrina, /Helicteroideae occupied the earliest branching position, followed by /Sterculioideae, /Brownlowioideae, /Tiliodeae, and /Dombeyoideae formed a clade sister to /Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.
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Affiliation(s)
- Tijana Cvetković
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Biodiversity Genomics Team, Guangxi University, Daxuedonglu 100, Nanning, Guangxi, 530005, China
| | - Fabiola Areces-Berazain
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Herbarium UPRRP, Department of Biology, University of Puerto Rico, San Juan PR 00925-2537, United States of America
| | - Damien D Hinsinger
- Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux (EPGV), 91000 Evry, France
| | - Daniel C Thomas
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, the Netherlands
| | - Santhana K Ganesan
- National Parks Board, Singapore Botanic Gardens, 1 Cluny Road, Singapore 259569, Singapore
| | - Joeri S Strijk
- Institute of Parasitology, Biology Centre CAS, Branišovská 1160/31, 37005 České Budějovice, Czech Republic.,Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, PO Box 959, 06000 Luang Prabang, Laos.,Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Jalan Tungku Link, BE1410, Brunei Darussalam
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15
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Shim H, Lee HJ, Lee J, Lee HO, Kim JH, Yang TJ, Kim NS. Plastid Genomes of the Early Vascular Plant Genus Selaginella Have Unusual Direct Repeat Structures and Drastically Reduced Gene Numbers. Int J Mol Sci 2021; 22:E641. [PMID: 33440692 DOI: 10.3390/ijms22020641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/20/2023] Open
Abstract
The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution. In this study, we sequenced and assembled the plastid genome (plastome) sequences of two Selaginella tamariscina individuals, as well as Selaginella stauntoniana and Selaginella involvens. Unlike the inverted repeat (IR) structures typically found in plant plastomes, Selaginella species had direct repeat (DR) structures, which were confirmed by Oxford Nanopore long-read sequence assembly. Comparative analyses of 19 lycophytes, including two Huperzia and one Isoetes species, revealed unique phylogenetic relationships between Selaginella species and related lycophytes, reflected by structural rearrangements involving two rounds of large inversions that resulted in dynamic changes between IR and DR blocks in the plastome sequence. Furthermore, we present other uncommon characteristics, including a small genome size, drastic reductions in gene and intron numbers, a high GC content, and extensive RNA editing. Although the 16 Selaginella species examined may not fully represent the genus, our findings suggest that Selaginella plastomes have undergone unique evolutionary events yielding genomic features unparalleled in other lycophytes, ferns, or seed plants.
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16
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Zhang R, Xu B, Li J, Zhao Z, Han J, Lei Y, Yang Q, Peng F, Liu ZL. Transit From Autotrophism to Heterotrophism: Sequence Variation and Evolution of Chloroplast Genomes in Orobanchaceae Species. Front Genet 2020; 11:542017. [PMID: 33133143 PMCID: PMC7573133 DOI: 10.3389/fgene.2020.542017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/07/2020] [Indexed: 01/15/2023] Open
Abstract
The family Orobanchaceae including autotrophic, hemiparasitic, and holoparasitic species, is becoming a key taxa to study the evolution of chloroplast genomes in different lifestyles. But the early evolutionary trajectory in the transit from autotrophism to hemiparasitism still maintains unclear for the inadequate sampling. In this study, we compared 50 complete chloroplast genomes in Orobanchaceae, containing four newly sequenced plastomes from hemiparasitic Pedicularis, to elucidate the sequence variation patterns in the evolution of plastomes. Contrasted to the sequence and structural hypervariabilities in holoparasites, hemiparasitic plastomes exhibited high similarity to those of autotrophs in gene and GC contents. They are generally characterized with functional or physical loss of ndh/tRNA genes and the inverted small-single-copy region. Gene losses in Orobanchaceae were lineage-specific and convergent, possibly related to structural reconfiguration and expansion/contraction of the inverted region. Pseudogenization of ndh genes was unique in hemiparasites. At least in Pedicularis, the ndhF gene might be most sensitive to the environmental factors and easily pseudogenized when autotrophs transit to hemiparasites. And the changes in gene contents and structural variation potentially deeply rely on the feeding type. Selective pressure, together with mutational bias, was the dominant factor of shaping the codon usage patterns. The relaxed selective constraint, potentially with genome-based GC conversion (gBGC) and preferential codon usage, drive the fluctuation of GC contents among taxa with different lifestyles. Phylogenetic analysis in Orobanchaceae supported that parasitic species were single-originated while holoparasites were multiple-originated. Overall, the comparison of plastomes provided a good opportunity to understand the evolution process in Orobanchaceae with different lifestyles.
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Affiliation(s)
- Ruiting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Bei Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jianfang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jie Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Yunjing Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Qian Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Fangfang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
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17
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Pischl PH, Burke SV, Bach EM, Duvall MR. Plastome phylogenomics and phylogenetic diversity of endangered and threatened grassland species (Poaceae) in a North American tallgrass prairie. Ecol Evol 2020; 10:7602-7615. [PMID: 32760551 PMCID: PMC7391303 DOI: 10.1002/ece3.6484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
Native grasslands are one of the most endangered ecosystems in North America. In this study, we examined the ecological and evolutionary roles of endangered and threatened (e/t) grasses by establishing robust evolutionary relationships with other nonthreatened native and introduced grass species of the community. We hypothesized that the phylogenomic distribution of e/t species of grasses in Illinois would be phylogenetically clustered because closely related species would be vulnerable to the same threats and have similar requirements for survival. This study presents the first time a phylogeny based on complete plastome DNA of Poaceae was analyzed by phylogenetic diversity analysis. To avoid the disturbance of e/t populations, DNA was extracted from herbarium specimens. Next-generation sequencing (NGS) techniques were used to sequence DNA of plastid genomes (plastomes). The resulting phylogenomic tree was analyzed by phylogenetic diversity metrics. The extracted DNA successfully produced complete plastomes demonstrating that herbarium material is a practical source of DNA for genomic studies. The phylogenomic tree was strongly supported and defined Dichanthelium as a separate clade from Panicum. The phylogenetic metrics revealed phylogenetic clustering of e/t species, confirming our hypothesis.
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Affiliation(s)
- Phyllis H. Pischl
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinoisUSA
| | - Sean V. Burke
- Center for Translational Data ScienceUniversity of ChicagoChicagoIllinoisUSA
| | | | - Melvin R. Duvall
- Department of Biological SciencesNorthern Illinois UniversityDeKalbIllinoisUSA
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18
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Ji Y, Liu C, Yang J, Jin L, Yang Z, Yang JB. Ultra-Barcoding Discovers a Cryptic Species in Paris yunnanensis (Melanthiaceae), a Medicinally Important Plant. Front Plant Sci 2020; 11:411. [PMID: 32391031 PMCID: PMC7189017 DOI: 10.3389/fpls.2020.00411] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/23/2020] [Indexed: 05/07/2023]
Abstract
Ultra-barcoding is a technique using whole plastomes and nuclear ribosomal DNA (nrDNA) sequences for plant species identification. Paris yunnanensis is a medicinal plant of great economic importance for the pharmaceutical industry. However, the alpha taxonomy of P. yunnanensis is still uncertain, hindering effective conservation and management of the germplasm. To resolve long-standing taxonomic disputes regarding this species, we newly generated the complete plastomes and nrDNA sequences from 22 P. yunnanensis accessions. Ultra-barcoding analyses suggest that P. yunnanensis as currently circumscribed is made up of two distinct genetic lineages, corresponding to the two phenotypes ("typical" and "high stem" form) identified early in our study. With distinct morphologies and distribution, the "high stem" form should be recognized as a previously unrecognized species; here it is described as a new species, P. liiana sp. nov. Moreover, the ultra-barcoding data do not support treatment of P. yunnanensis as a conspecific variety under Paris polyphylla. Our study represents a guiding practical application of ultra-barcoding for discovery of cryptic species in taxonomically challenging plant taxa. The findings highlight the great potential of ultra-barcoding as an effective tool for resolving perplexing problems in plant taxonomy.
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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 Populations, 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
| | - Jin 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 Sciences, Yunnan University, Kunming, China
| | - Lei Jin
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhenyan Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Shen J, Zhang X, Landis JB, Zhang H, Deng T, Sun H, Wang H. Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses. Front Plant Sci 2020; 11:376. [PMID: 32351518 PMCID: PMC7174903 DOI: 10.3389/fpls.2020.00376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/16/2020] [Indexed: 05/24/2023]
Abstract
Dolomiaea is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), along with a total of 51-61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of Dolomiaea as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, rpoC2 and ycf1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.
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Affiliation(s)
- Jun Shen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jacob B. Landis
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, 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
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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Cascales J, Bracco M, Garberoglio MJ, Poggio L, Gottlieb AM. Integral Phylogenomic Approach over Ilex L. Species from Southern South America. Life (Basel) 2017; 7:E47. [PMID: 29165335 DOI: 10.3390/life7040047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/03/2017] [Accepted: 11/16/2017] [Indexed: 11/17/2022] Open
Abstract
The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I.paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses. We selected seven introns and nine IGSs as variable non-coding markers that were used in phylogenomic analyses. Eight extra IGSs were proposed as candidate markers. Southern South American species formed one lineage, except for I. paraguariensis, I. dumosa and I. argentina, which occupied intermediate positions among sampled taxa; Euroasiatic species formed two lineages. Some concordant relationships were retrieved from nuclear sequence data. We also conducted integral analyses, involving a supernetwork of molecular data, and a simultaneous analysis of quantitative and qualitative morphological and phytochemical characters, together with molecular data. The total evidence tree was used to study the evolution of non-molecular data, evidencing fifteen non-ambiguous synapomorphic character states and consolidating the relationships among southern South American species. More South American representatives should be incorporated to elucidate their origin.
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Lam VKY, Merckx VSFT, Graham SW. A few-gene plastid phylogenetic framework for mycoheterotrophic monocots. Am J Bot 2016; 103:692-708. [PMID: 27056932 DOI: 10.3732/ajb.1500412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/08/2016] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Few-gene studies with broad taxon sampling have provided major insights into phylogeny and underpin plant classification. However, they have typically excluded heterotrophic plants because of loss, pseudogenization, or rapid evolution of plastid genes. Here we performed a phylogenetic survey of three commonly retained plastid genes to assess their utility in placing mycoheterotrophs. METHODS We surveyed accD, clpP, and matK for 34 taxa from seven monocot families that include full mycoheterotrophs and a broad sampling of photosynthetic taxa. After screening for weak contaminants, we conducted phylogenetic analyses and characterized among-lineage rate variation. KEY RESULTS Likelihood analyses strongly supported local placements of fully mycoheterotrophic taxa for Corsiaceae, Iridaceae, Orchidaceae, and Petrosaviaceae, in positions consistent with other studies. Depression of likelihood bootstrap support values near mycoheterotrophic clades was alleviated when each mycoheterotrophic family was considered separately. Triuridaceae (Sciaphila) monophyly was recovered in a partitioned likelihood analysis, and the family then placed as sister to Cyclanthaceae-Pandanaceae. Burmanniaceae placed in Dioscoreales with weak to strong support depending on analysis details, and we inferred a plastid-based phylogeny for the family. Thismiaceae species may retain a plastid genome, based on accD retention. The inferred position of Thismiaceae is unstable, but was close to Taccaceae (Dioscoreales) in some analyses. CONCLUSIONS Long branches/elevated substitution rates, missing genes, and occasional contaminants are challenges for plastid-based phylogenetic inference with full mycoheterotrophs. However, most mycoheterotrophs can be readily integrated into the broad picture of plant phylogeny using several plastid genes and broad taxonomic sampling.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Ruhfel BR, Gitzendanner MA, Soltis PS, Soltis DE, Burleigh JG. From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes. BMC Evol Biol 2014; 14:23. [PMID: 24533922 PMCID: PMC3933183 DOI: 10.1186/1471-2148-14-23] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/13/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. RESULTS We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. CONCLUSIONS Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-7800, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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