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Ihsan A. Al-shehbaz - One of the best experts on this subject based on the ideXlab platform.
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Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity.
New Phytologist, 2019Co-Authors: Lachezar A. Nikolov, Ihsan A. Al-shehbaz, Philip Shushkov, Bruno Nevado, Xiangchao Gan, Dmitry A. Filatov, C. Donovan Bailey, Miltos TsiantisAbstract:Summary: The Brassicaceae family comprises c. 4000 species including economically important crops and the model plant Arabidopsis thaliana. Despite their importance, the relationships among major lineages in the family remain unresolved, hampering comparative research. Here, we inferred a Brassicaceae phylogeny using newly generated targeted enrichment sequence data of 1827 exons (> 940 000 bases) representing 63 species, as well as sequenced genome data of 16 species, together representing 50 of the 52 currently recognized Brassicaceae tribes. A third of the samples were derived from herbarium material, facilitating broad taxonomic coverage of the family. Six major clades formed successive sister groups to the rest of Brassicaceae. We also recovered strong support for novel relationships among tribes, and resolved the position of 16 taxa previously not assigned to a tribe. The broad utility of these phylogenetic results is illustrated through a comparative investigation of genome‐wide expression signatures that distinguish simple from complex leaves in Brassicaceae. Our study provides an easily extendable dataset for further advances in Brassicaceae systematics and a timely higher‐level phylogenetic framework for a wide range of comparative studies of multiple traits in an intensively investigated group of plants.
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Plastome phylogeny and early diversification of Brassicaceae
BMC Genomics, 2017Co-Authors: Xinyi Guo, Jianquan Liu, Guoqian Hao, Leyou Zhang, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Tao Ma, Quanjun Hu, Ihsan A. Al-shehbazAbstract:BackgroundThe family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.ResultsBayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.ConclusionsPlastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
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Plastome phylogeny and early diversification of Brassicaceae
BMC Genomics, 2017Co-Authors: Xinyi Guo, Jianquan Liu, Guoqian Hao, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Lei Zhang, Ihsan A. Al-shehbazAbstract:The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
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eLS - Brassicaceae (Mustard Family)
eLS, 2011Co-Authors: Ihsan A. Al-shehbazAbstract:The Brassicaceae (Cruciferae) or mustard family is a well-defined group of about 310 genera and some 3500 species distributed primarily in the temperate and alpine areas of all continents except Antarctia. It is most highly diversified in central and western Asia, Mediterranean Europe and western North America. This article discusses the economic importance of the family (food, oils, condiments, ornamentals and weeds) and role played by one of its weedy member, the model organism Arabidopsis thaliana, in the advancement of modern experimental biology. Here we also review the morphology, biogeography, ecology and phylogenetic relationship within Brassicaceae and to other families. We also cover the significance of molecular data in dividing the family into 48 monophyletic tribes and in determining its major lineages. Finally, a brief discussion is presented on the whole-genome duplication events and their possible role in the radiation and diversification of the family. Key Concepts: Model organisms, such as the mustard Arabidopsis thaliana, should always be used to understand complex biological phenomena in other organisms. Owing to extensive morphological convergence, molecular data alone provide the most reliable and solid phylogenetic classification within the Brassicaceae. Invasive weeds of the mustard family can only be understood by closer studies of their immediate wild relatives. Germplasm conservation centres of the economically important Brassicaceae should substantially increase their efforts to save their rapidly disappearing wild relatives. Vegetable crops of Brassica should be thoroughly tested to determine their medicinal values in combating cancer and other diseases. Keywords: mustard family; Brassicaceae; Cruciferae; economic importance; Arabidopsis; reproductive biology; phylogeny; biogeography
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Arabidopsis family ties: molecular phylogeny and age estimates in Brassicaceae
Taxon, 2009Co-Authors: Andreas Franzke, Dmitry A. German, Ihsan A. Al-shehbaz, Klaus MummenhoffAbstract:The Brassicaceae family is of great scientific interest because it contains the plant model organism Arabidopsis thaliana. Currently, contemporary plant research activities expand to other Brassicaceae taxa. Despite that, the phylogeny of this family is only partly understood. The present study deepens our understanding of a family-wide phylogeny by using two new approaches in phylogenetic family-wide research. We used a molecular marker from the mitochondrial genome and utilised a relaxed molecular dating method. Our data generally confirms a recent tribal alignment of Brassicaceae. We present for the first time a biogeographical scenario for the broad-scale Brassicaceae evolution. We suggest that Brassicaceae most likely evolved some 19 mya in or near the eastern Mediterranean region from a common ancestor of its sister family Cleomaceae. The early Brassicaceae formed a lineage adapted to more open/drier habitats than its capparoid progenitors. The early Brassicaceae evolution was very rapid and the radiation was most likely driven by climatic changes that created open habitats and the well-documented expansion of open grass-dominated ecosystems. Moreover, our dating suggests that the radiation events correlate with an ancient genome duplication in the early history of the family, which is evidenced by recent genomic studies.
Marcus A. Koch - One of the best experts on this subject based on the ideXlab platform.
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Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events.
Annals of Botany, 2019Co-Authors: Xiao-chen Huang, Dmitry A. German, Marcus A. KochAbstract:BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Molecular Resources from Transcriptomes in the Brassicaceae Family.
Frontiers in Plant Science, 2017Co-Authors: Lua Lopez, Patrick P Edger, Eva M. Wolf, J. Chris Pires, Marcus A. KochAbstract:The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed SSRs (single short repeats) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family. Moreover, we selected the genus Cochlearia to test the transferability and polymorphism of these markers among species. Additionally, we annotated Cochlearia pyrenaica transcriptome in order to identify the position of each of the mined SSRs. While we introduce a new set of tools that will further enable evolutionary studies across the Brassicaceae, we also discuss some broader aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR markers with their respective primers in 19 Brassicaceae species and a high quality annotated transcriptome for Cochlearia pyrenaica. As indicated by our transferability test with the genus Cochlearia these SSRs are transferable to species within the genus increasing exponentially the number of targeted species. Also, our polymorphism results showed substantial levels of variability for these markers. Finally, despite its complex evolutionary history, SSR evolution across the Brassicaceae family are highly conserved and we found no deviation from patterns reported in other Angiosperms.
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resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution
Molecular Biology and Evolution, 2016Co-Authors: Chien Hsun Huang, Marcus A. Koch, Patrick P Edger, Yi Hu, Liping Zeng, Ning Zhang, Qiang Zhang, Ihsan A Alshehbaz, Chris J Pires, Yang ZhongAbstract:Brassicaceae is one of the most diverse and economically valuable angiosperm families with widely cultivated vegetable crops and scientifically important model plants, such as Arabidopsis thaliana. The evolutionary history, ecological, morphological, and genetic diversity, and abundant resources and knowledge of Brassicaceae make it an excellent model family for evolutionary studies. Recent phylogenetic analyses of the family revealed three major lineages (I, II, and III), but relationships among and within these lineages remain largely unclear. Here, we present a highly supported phylogeny with six major clades using nuclear markers from newly sequenced transcriptomes of 32 Brassicaceae species and large data sets from additional taxa for a total of 55 species spanning 29 out of 51 tribes. Clade A consisting of Lineage I and Macropodium nivale is sister to combined Clade B (with Lineage II and others) and a new Clade C. The ABC clade is sister to Clade D with species previously weakly associated with Lineage II and Clade E (Lineage III) is sister to the ABCD clade. Clade F (the tribe Aethionemeae) is sister to the remainder of the entire family. Molecular clock estimation reveals an early radiation of major clades near or shortly after the Eocene–Oligocene boundary and subsequent nested divergences of several tribes of the previously polytomous Expanded Lineage II. Reconstruction of ancestral morphological states during the Brassicaceae evolution indicates prevalent parallel (convergent) evolution of several traits over deep times across the entire family. These results form a foundation for future evolutionary analyses of structures and functions across Brassicaceae.
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a time calibrated road map of Brassicaceae species radiation and evolutionary history
The Plant Cell, 2015Co-Authors: Nora Hohmann, Eva M. Wolf, Martin A. Lysak, Marcus A. KochAbstract:The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.
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The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae
Molecular Biology and Evolution, 2008Co-Authors: Martin A. Lysak, Marcus A. Koch, Jeremy M. Beaulieu, Armin Meister, Ilia J. LeitchAbstract:This paper reports new genome size (GS) data for more than 100 cruciferous species in addition to previously published C-values to give a data set comprising 185 Brassicaceae taxa. Evolution of GS was analyzed within a phylogenetic framework. Approximately 50% of crucifer taxa analyzed showed a decrease in GS compared with the ancestral genome size inferred for Brassicaceae. The remaining species showed an increase in GS although this was generally moderate. We also found that GS has not changed substantially through time and most likely evolves passively. It is suggested that mechanisms to suppress amplification and to eliminate amplified DNA must be active in Brassicaceae.
Xinyi Guo - One of the best experts on this subject based on the ideXlab platform.
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Plastome phylogeny and early diversification of Brassicaceae
BMC Genomics, 2017Co-Authors: Xinyi Guo, Jianquan Liu, Guoqian Hao, Leyou Zhang, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Tao Ma, Quanjun Hu, Ihsan A. Al-shehbazAbstract:BackgroundThe family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.ResultsBayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.ConclusionsPlastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
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Plastome phylogeny and early diversification of Brassicaceae
BMC Genomics, 2017Co-Authors: Xinyi Guo, Jianquan Liu, Guoqian Hao, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Lei Zhang, Ihsan A. Al-shehbazAbstract:The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family. Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
Ikuko Hara-nishimura - One of the best experts on this subject based on the ideXlab platform.
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NAI2 and TSA1 Drive Differentiation of Constitutive and Inducible ER Body Formation in Brassicaceae
Plant and Cell Physiology, 2020Co-Authors: Natalia Stefanik, Jakub Bizan, Alwine Wilkens, Katarzyna Tarnawska-glatt, Shino Goto-yamada, Kazimierz Strzałka, Mikio Nishimura, Ikuko Hara-nishimura, Kenji YamadaAbstract:Brassicaceae and closely related species develop unique endoplasmic reticulum (ER)-derived structures called ER bodies, which accumulate β-glucosidases/myrosinases that are involved in chemical defense. There are two different types of ER bodies: ER bodies constitutively present in seedlings (cER bodies) and ER bodies in rosette leaves induced by treatment with the wounding hormone jasmonate (JA) (iER bodies). Here, we show that At-α whole-genome duplication (WGD) generated the paralogous genes NAI2 and TSA1, which consequently drive differentiation of cER bodies and iER bodies in Brassicaceae plants. In Arabidopsis, NAI2 is expressed in seedlings where cER bodies are formed, whereas TSA1 is expressed in JA-treated leaves where iER bodies are formed. We found that the expression of NAI2 in seedlings and the JA inducibility of TSA1 are conserved across other Brassicaceae plants. The accumulation of NAI2 transcripts in Arabidopsis seedlings is dependent on the transcription factor NAI1, whereas the JA induction of TSA1 in rosette leaves is dependent on MYC2, MYC3 and MYC4. We discovered regions of microsynteny, including the NAI2/TSA1 genes, but the promoter regions are differentiated between TSA1 and NAI2 genes in Brassicaceae. This suggests that the divergence of function between NAI2 and TSA1 occurred immediately after WGD in ancestral Brassicaceae plants to differentiate the formation of iER and cER bodies. Our findings indicate that At-α WGD enabled diversification of defense strategies, which may have contributed to the massive diversification of Brassicaceae plants.
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Endoplasmic reticulum-derived bodies enable a single-cell chemical defense in Brassicaceae plants.
Communications biology, 2020Co-Authors: Kenji Yamada, Shino Goto-yamada, Mikio Nishimura, Akiko Nakazaki, Tadashi Kunieda, Keiko Kuwata, Atsushi J. Nagano, Ikuko Hara-nishimuraAbstract:Brassicaceae plants have a dual-cell type of chemical defense against herbivory. Here, we show a novel single-cell defense involving endoplasmic reticulum (ER)-derived organelles (ER bodies) and the vacuoles. We identify various glucosinolates as endogenous substrates of the ER-body β-glucosidases BGLU23 and BGLU21. Woodlice strongly prefer to eat seedlings of bglu23 bglu21 or a glucosinolate-deficient mutant over wild-type seedlings, confirming that the β-glucosidases have a role in chemical defense: production of toxic compounds upon organellar damage. Deficiency of the Brassicaceae-specific protein NAI2 prevents ER-body formation, which results in a loss of BGLU23 and a loss of resistance to woodlice. Hence, NAI2 that interacts with BGLU23 is essential for sequestering BGLU23 in ER bodies and preventing its degradation. Artificial expression of NAI2 and BGLU23 in non-Brassicaceae plants results in the formation of ER bodies, indicating that acquisition of NAI2 by Brassicaceae plants is a key step in developing their single-cell defense system. Kenji Yamada et al. describe a single-cell chemical defense strategy in Brassicaceae plants that requires formation of endoplasmic reticulum-derived organelles for the accumulation of β-glucosidases. They find that seedlings lacking a specific β-glucosidase lose their resistance to predation by woodlice.
Martin A. Lysak - One of the best experts on this subject based on the ideXlab platform.
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Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae
Frontiers in Plant Science, 2020Co-Authors: Nora Walden, Thu Phuong Nguyen, Terezie Mandáková, Martin A. Lysak, M.e. SchranzAbstract:The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.
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diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention
Plant Journal, 2017Co-Authors: Terezie Mandáková, Michael S Barker, Martin A. LysakAbstract:Summary Hybridization and polyploidy followed by genome-wide diploidization significantly impacted the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization impacted post-polyploid gene retention. Sixteen species representing ten Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of Brassicaceae genomic data indicate that the extant chromosome number variation in many plant groups, and especially monophyletic taxa with multiple base chromosome numbers, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests that patterns of post-polyploid genome evolution are predictable. This article is protected by copyright. All rights reserved.
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diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention
bioRxiv, 2017Co-Authors: Terezie Mandáková, Michael S Barker, Martin A. LysakAbstract:Hybridization and polyploidy followed by genome-wide diploidization significantly impacted the diversification of land plants. The ancient At-α whole-genome duplication (WGD) preceded the diversification of crucifers (Brassicaceae). Some genera and tribes also experienced younger, mesopolyploid WGDs concealed by subsequent genome diploidization. Here we tested if multiple base chromosome numbers originated due to genome diploidization after independent mesopolyploid WGDs and how diploidization impacted post-polyploid gene retention. Sixteen species representing ten Brassicaceae tribes were analyzed by comparative chromosome painting and/or whole-transcriptome analysis of gene age distributions and phylogenetic analyses of gene duplications. Overall, we found evidence for at least 13 independent mesopolyploidies followed by different degrees of diploidization across the Brassicaceae. New mesotetraploid events were uncovered for tribes Anastaticeae, Iberideae and Schizopetaleae, and mesohexaploid WGDs for Cochlearieae and Physarieae. In contrast, we found convergent patterns of gene retention and loss among these independent WGDs. Our combined analyses of Brassicaceae genomic data indicate that the extant chromosome number variation in many plant groups, and especially polybasic but monophyletic taxa, can result from clade-specific genome duplications followed by diploidization. Our observation of parallel gene retention and loss across multiple independent WGDs provides one of the first multi-species tests that post-polyploid genome evolution is predictable.
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a time calibrated road map of Brassicaceae species radiation and evolutionary history
The Plant Cell, 2015Co-Authors: Nora Hohmann, Eva M. Wolf, Martin A. Lysak, Marcus A. KochAbstract:The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ∼20 million years ago, coinciding with the Oligocene-to-Miocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.
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The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae
Molecular Biology and Evolution, 2008Co-Authors: Martin A. Lysak, Marcus A. Koch, Jeremy M. Beaulieu, Armin Meister, Ilia J. LeitchAbstract:This paper reports new genome size (GS) data for more than 100 cruciferous species in addition to previously published C-values to give a data set comprising 185 Brassicaceae taxa. Evolution of GS was analyzed within a phylogenetic framework. Approximately 50% of crucifer taxa analyzed showed a decrease in GS compared with the ancestral genome size inferred for Brassicaceae. The remaining species showed an increase in GS although this was generally moderate. We also found that GS has not changed substantially through time and most likely evolves passively. It is suggested that mechanisms to suppress amplification and to eliminate amplified DNA must be active in Brassicaceae.