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Paiva MISDEL, Amorim BS, Albuquerque PM, Maciel JR. Climatic niche shift after range expansion of Eustachys (Poaceae). AN ACAD BRAS CIENC 2024; 96:e20220414. [PMID: 38865504 DOI: 10.1590/0001-3765202420220414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/17/2023] [Indexed: 06/14/2024] Open
Abstract
Eustachys presents lower diversity in the Old World than in the Neotropics and it occurs disjunctly between main tropical regions. This qualifies Eustachys as a good model to test whether lineages expand their niches during the process of range expansion. We performed ancestral range reconstruction, compared environmental spaces of the different geographic areas and assessed bioclimatic trait evolution. Ancestral range reconstruction indicated that most speciation in Eustachys occurred in the South America. Ancestral climatic niches of the New World are different from those of African and Australasia lineages. Our results show that Eustachys experienced niche expansion when it reached the New World. Evolutionary history of Eustachys illustrates how the range expansion promoted climatic niche shifts, which could drive unbalanced species richness of the genus among different tropical regions.
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Affiliation(s)
- Maria Izabel S DE Lima Paiva
- Prefeitura da Cidade do Recife, Jardim Botânico do Recife, BR 232, Km 7, s/n, 50000-230 Recife, PE, Brazil
- Faculdade Frassinetti do Recife, Departamento de Biologia, Av. Conde da Boa Vista, 921, 50050-900 Recife, PE, Brazil
| | - Bruno S Amorim
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Escola Superior de Ciências da Saúde, Av. Carvalho Leal, 1777, 69065-001 Manaus, AM, Brazil
- Museu da Amazônia, Av. Margarita, 6305, 69099-415 Manaus, AM, Brazil
- Herbário IFMG, Instituto Federal de Minas Gerais - Campus Bambuí, Departamento de Ciências e Linguagens, Rodovia Bambuí/Medeiros, Km 05, s/n, 38900-000 Bambuí, MG, Brazil
| | - Patrícia M Albuquerque
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Escola Superior de Ciências da Saúde, Av. Carvalho Leal, 1777, 69065-001 Manaus, AM, Brazil
| | - Jefferson R Maciel
- Prefeitura da Cidade do Recife, Jardim Botânico do Recife, BR 232, Km 7, s/n, 50000-230 Recife, PE, Brazil
- Programa de Pós-Graduação em Biodiversidade, Universidade Federal Rural de Pernambuco, Rua Dom Manoel de Medeiros, s/n, 52171-930 Recife, PE, Brazil
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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Hu Y, Sun Y, Zhu QH, Fan L, Li J. Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years. Curr Genomics 2023; 23:369-384. [PMID: 37920556 PMCID: PMC10173419 DOI: 10.2174/1389202924666221201140603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/02/2022] [Accepted: 10/19/2022] [Indexed: 12/11/2022] Open
Abstract
The first complete chloroplast genome of rice (Oryza sativa) was published in 1989, ushering in a new era of studies of chloroplast genomics in Poaceae. Progresses in Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) technologiesand in the development of genome assembly software, have significantly advanced chloroplast genomics research. Poaceae is one of the most targeted families in chloroplast genome research because of its agricultural, ecological, and economic importance. Over the last 30 years, 2,050 complete chloroplast genome sequences from 40 tribes and 282 genera have been generated, most (97%) of them in the recent ten years. The wealth of data provides the groundwork for studies on species evolution, phylogeny, genetic transformation, and other aspects of Poaceae chloroplast genomes. As a result, we have gained a deeper understanding of the properties of Poaceae chloroplast genomes. Here, we summarize the achievements of the studies of the Poaceae chloroplast genomes and envision the challenges for moving the area ahead.
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Affiliation(s)
- Yiyu Hu
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Yanqing Sun
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jianhua Li
- Department of Rehabilitation Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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High-quality chromosome-scale de novo assembly of the Paspalum notatum 'Flugge' genome. BMC Genomics 2022; 23:293. [PMID: 35410159 PMCID: PMC9004155 DOI: 10.1186/s12864-022-08489-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Paspalum notatum 'Flugge' is a diploid with 20 chromosomes (2n = 20) multi-purpose subtropical herb native to South America and has a high ecological significance. It is currently widely planted in tropical and subtropical regions. Despite the gene pool of P. notatum 'Flugge' being unearthed to a large extent in the past decade, no details about the genomic information of relevant species in Paspalum have been reported. In this study, the complete genome information of P. notatum was established and annotated through sequencing and de novo assembly of its genome. RESULTS The latest PacBio third-generation HiFi assembly and sequencing revealed that the genome size of P. notatum 'Flugge' is 541 M. The assembly result is the higher index among the genomes of the gramineous family published so far, with a contig N50 = 52Mbp, scaffold N50 = 49Mbp, and BUSCOs = 98.1%, accounting for 98.5% of the estimated genome. Genome annotation revealed 36,511 high-confidence gene models, thus providing an important resource for future molecular breeding and evolutionary research. A comparison of the genome annotation results of P. notatum 'Flugge' with other closely related species revealed that it had a close relationship with Zea mays but not close compared to Brachypodium distachyon, Setaria viridis, Oryza sativa, Puccinellia tenuiflora, Echinochloa crusgalli. An analysis of the expansion and contraction of gene families suggested that P. notatum 'Flugge' contains gene families associated with environmental resistance, increased reproductive ability, and molecular evolution, which explained its excellent agronomic traits. CONCLUSION This study is the first to report the high-quality chromosome-scale-based genome of P. notatum 'Flugge' assembled using the latest PacBio third-generation HiFi sequencing reads. The study provides an excellent genetic resource bank for gramineous crops and invaluable perspectives regarding the evolution of gramineous plants.
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Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
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Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
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Guo XX, Qu XJ, Zhang XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae). BIOLOGY 2022; 11:biology11010063. [PMID: 35053061 PMCID: PMC8773369 DOI: 10.3390/biology11010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022]
Abstract
Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C4 Stipagrostis and C3 Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.
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Affiliation(s)
| | | | - Xue-Jie Zhang
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Z.); (S.-J.F.); Tel.: +86-531-86180718 (S.-J.F.)
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Ferreira RCU, da Costa Lima Moraes A, Chiari L, Simeão RM, Vigna BBZ, de Souza AP. An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures. FRONTIERS IN PLANT SCIENCE 2021; 12:770461. [PMID: 34966402 PMCID: PMC8710810 DOI: 10.3389/fpls.2021.770461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
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Affiliation(s)
| | - Aline da Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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Bhatt P, Thaker V. A comparative study on 193 plastomes of Poaceae for validity and implications of individual barcode genes and concatenated protein coding sequences with selected plastomes of grasses from the desert of India. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Cheon SH, Woo MA, Jo S, Kim YK, Kim KJ. The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae). PLANTS 2021; 10:plants10081517. [PMID: 34451562 PMCID: PMC8400354 DOI: 10.3390/plants10081517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022]
Abstract
The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.
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Wei X, Li X, Chen T, Chen Z, Jin Y, Malik K, Li C. Complete chloroplast genomes of Achnatherum inebrians and comparative analyses with related species from Poaceae. FEBS Open Bio 2021; 11:1704-1718. [PMID: 33932143 PMCID: PMC8167873 DOI: 10.1002/2211-5463.13170] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/24/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
This article reports the complete chloroplast genome of Achnatherum inebrians, a poisonous herb that is widely distributed in the rangelands of Northern China. The genome is 137 714 bp in total and consists of a large single‐copy (81 758 bp) region and small single‐copy (12 682 bp) region separated by a pair of inverted repeats (21 637 bp). The genome contains 130 genes, including 84 protein‐coding genes, 38 tRNA genes and 8 ribosomal RNA genes, and the guanine + cytosine content is 36.17%. We subsequently performed comparative analysis of complete genomes from A. inebrians and other Poaceae‐related species from GenBank. Thirty‐eight simple sequence repeats were identified, further demonstrating rapid evolution in Poaceae. Finally, the phylogenetic trees of 37 species of Poaceae and 2 species of Amaranthaceae were constructed by using maximum likelihood and Bayesian inference methods, based on the genes of the complete chloroplast genome. We identified hotspots that can be used as molecular markers and barcodes for phylogenetic analysis, as well as for species identification. Phylogenetic analysis indicated that A. inebrians is a member of the genus Stipa rather than Achnatherum.
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Affiliation(s)
- Xuekai Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Xiuzhang Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining, China
| | - Taixiang Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Zhenjiang Chen
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Yuanyuan Jin
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Kamran Malik
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
| | - Chunjie Li
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Centre of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, China
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Cui F, Taier G, Li M, Dai X, Hang N, Zhang X, Wang X, Wang K. The genome of the warm-season turfgrass African bermudagrass (Cynodon transvaalensis). HORTICULTURE RESEARCH 2021; 8:93. [PMID: 33931599 PMCID: PMC8087826 DOI: 10.1038/s41438-021-00519-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 05/03/2023]
Abstract
Cynodon species can be used for multiple purposes and have high economic and ecological significance. However, the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood, partially due to the limited availability of genomic resources. In this study, we report a chromosome-scale genome assembly of a diploid Cynodon species, C. transvaalensis, obtained by combining Illumina and Nanopore sequencing, BioNano, and Hi-C. The assembly contains 282 scaffolds (~423.42 Mb, N50 = 5.37 Mb), which cover ~93.2% of the estimated genome of C. transvaalensis (~454.4 Mb). Furthermore, 90.48% of the scaffolds (~383.08 Mb) were anchored to nine pseudomolecules, of which the largest was 60.78 Mb in length. Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates, typically with dry summers. The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily, in particular, the Cynodonteae tribe, but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.
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Affiliation(s)
- Fengchao Cui
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Geli Taier
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Manli Li
- Department of Breeding and Seed Science, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaoxia Dai
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Nan Hang
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xunzhong Zhang
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Xiangfeng Wang
- National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100913, China.
| | - Kehua Wang
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Orton LM, Barberá P, Nissenbaum MP, Peterson PM, Quintanar A, Soreng RJ, Duvall MR. A 313 plastome phylogenomic analysis of Pooideae: Exploring relationships among the largest subfamily of grasses. Mol Phylogenet Evol 2021; 159:107110. [PMID: 33609709 DOI: 10.1016/j.ympev.2021.107110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae). We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the "mask alignment" tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.
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Affiliation(s)
- Lauren M Orton
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA.
| | - Patricia Barberá
- Department of Africa and Madagascar, Missouri Botanical Garden, St. Louis, MO 63110, USA
| | - Matthew P Nissenbaum
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Paul M Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Alejandro Quintanar
- Herbario MA, Unidad de Herbarios, Real Jardín Botánico de Madrid CSIC, 28014 Madrid, Spain
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington DC 20013-7012, USA
| | - Melvin R Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA; Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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13
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Kellogg EA, Abbott JR, Bawa KS, Gandhi KN, Kailash BR, Ganeshaiah K, Shrestha UB, Raven P. Checklist of the grasses of India. PHYTOKEYS 2020; 163:1-560. [PMID: 37397271 PMCID: PMC10311516 DOI: 10.3897/phytokeys.163.38393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 01/22/2020] [Indexed: 07/04/2023]
Abstract
A checklist of the grasses of India is presented, as compiled from survey of all available literature. Of the twelve subfamilies of grasses, ten are represented in India. Most subfamilies have been examined by taxonomic experts for up-to-date nomenclature. The list includes 1506 species plus infraspecific taxa and presents information on types, synonyms, distribution within India, and habit. Twelve new combinations are made, viz. Arctopoa tibetica (Munro ex Stapf) Prob. var. aristulata (Stapf) E.A. Kellogg, comb. nov.; Chimonocalamus nagalandianus (H.B. Naithani) L.G. Clark, comb. nov.; Chionachne digitata (L.f.) E.A. Kellogg, comb. nov.; Chionachne wallichiana (Nees) E.A. Kellogg, comb. nov.; Dinebra polystachyos (R. Br.) E.A. Kellogg, comb. nov.; Moorochloa eruciformis (Sm.) Veldkamp var. divaricata (Basappa & Muniv.) E.A. Kellogg, comb. nov.; Phyllostachys nigra (Lodd. ex Lindl.) Munro var. puberula (Miq.) Kailash, comb. & stat. nov.; Tzveleviochloa schmidii (Hook. f.) E.A. Kellogg, comb. nov.; Urochloa lata (Schumach.) C.E. Hubb. var. pubescens (C.E. Hubb.) E.A. Kellogg, comb. nov.; Urochloa ramosa (L.) T.Q. Nguyen var. pubescens (Basappa & Muniy.) E.A. Kellogg, comb. nov.; Urochloa semiundulata (Hochst. ex A. Rich.) Ashalatha & V.J. Nair var. intermedia (Basappa & Muniy.) E.A. Kellogg, comb. nov.
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Affiliation(s)
| | - J. Richard Abbott
- Missouri Botanical GardenSt. LouisUnited States of America
- Missouri Botanical GardenSt. Louis, MOUnited States of America
| | - Kamaljit S. Bawa
- University of Massachusetts, BostonBostonUnited States of America
| | | | - B. R. Kailash
- 5Ashoka Trust for Research in Ecology and the Environment (ATREE)BangaloreIndia
| | | | | | - Peter Raven
- Missouri Botanical GardenSt. LouisUnited States of America
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14
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Orton LM, Fitzek E, Feng X, Grayburn WS, Mower JP, Liu K, Zhang C, Duvall MR, Yin Y. Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3361-3373. [PMID: 32206790 DOI: 10.1093/jxb/eraa149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/19/2020] [Indexed: 05/22/2023]
Abstract
The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.
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Affiliation(s)
- Lauren M Orton
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Elisabeth Fitzek
- Biology/Computational Biology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology-CeBiTec, Bielefeld, Germany
| | - Xuehuan Feng
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - W Scott Grayburn
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Yanbin Yin
- Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
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15
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Gallaher TJ, Adams DC, Attigala L, Burke SV, Craine JM, Duvall MR, Klahs PC, Sherratt E, Wysocki WP, Clark LG. Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae). Evolution 2019; 73:927-946. [PMID: 30874302 DOI: 10.1111/evo.13722] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/15/2019] [Indexed: 01/19/2023]
Abstract
Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.
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Affiliation(s)
- Timothy J Gallaher
- Department of Biology, University of Washington, Seattle, Washington, 98195
| | - Dean C Adams
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
| | - Lakshmi Attigala
- Plant Sciences Institute, Iowa State University, Ames, Iowa, 50011
| | - Sean V Burke
- Center for Data Intensive Sciences, University of Chicago, Chicago, Illinois, 60615
| | | | - Melvin R Duvall
- Plant Molecular and Bioinformatics Center/Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, 60115
| | - Phillip C Klahs
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
| | - Emma Sherratt
- Department of Ecology & Evolutionary Biology, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - William P Wysocki
- Center for Data Intensive Sciences, University of Chicago, Chicago, Illinois, 60615
| | - Lynn G Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
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16
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VanBuren R, Wai CM, Keilwagen J, Pardo J. A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum. PLANT DIRECT 2018. [PMID: 31245697 DOI: 10.1101/378943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A draft genome of Oropetium was recently sequenced, but the lack of a chromosome-scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into 10 chromosomes using high-throughput chromatin conformation capture (Hi-C) based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. Comparison between the Sorghum and Oropetium genomes revealed a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass-comparative genomic community and further establish Oropetium as a model resurrection plant.
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Affiliation(s)
- Robert VanBuren
- Department of Horticulture Michigan State University East Lansing Michigan
- Plant Resilience Institute Michigan State University East Lansing Michigan
| | - Ching Man Wai
- Department of Horticulture Michigan State University East Lansing Michigan
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Jeremy Pardo
- Department of Plant Biology Michigan State University East Lansing Michigan
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17
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Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C. Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots. AMERICAN JOURNAL OF BOTANY 2018; 105:1888-1910. [PMID: 30368769 DOI: 10.1002/ajb2.1178] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth. KEY RESULTS Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome-scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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Affiliation(s)
- Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | | | - Daniel Spalink
- Department of Ecosystem Science, Texas A&M University, College Station, Texas, 77840, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Vivienne K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Chodon Sass
- The University and Jepson Herbarium, University of California-Berkeley, Berkeley, California, 94720, USA
| | - William J D Iles
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Danilo José Lima de Sousa
- Departamento de Ciéncias Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, 44036-900, Brazil
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, 65211, USA
| | - Wendy B Zomlefer
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, USA
| | - Maria A Gandolfo
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | | | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Chelsea D Specht
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 14853, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia, 26506, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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18
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VanBuren R, Wai CM, Keilwagen J, Pardo J. A chromosome-scale assembly of the model desiccation tolerant grass Oropetium thomaeum. PLANT DIRECT 2018; 2:e00096. [PMID: 31245697 PMCID: PMC6508818 DOI: 10.1002/pld3.96] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 05/19/2023]
Abstract
Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A draft genome of Oropetium was recently sequenced, but the lack of a chromosome-scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into 10 chromosomes using high-throughput chromatin conformation capture (Hi-C) based chromatin interactions. A combination of high-resolution RNAseq data and homology-based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. Comparison between the Sorghum and Oropetium genomes revealed a surprising degree of chromosome-level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass-comparative genomic community and further establish Oropetium as a model resurrection plant.
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Affiliation(s)
- Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMichigan
- Plant Resilience InstituteMichigan State UniversityEast LansingMichigan
| | - Ching Man Wai
- Department of HorticultureMichigan State UniversityEast LansingMichigan
| | - Jens Keilwagen
- Institute for Biosafety in Plant BiotechnologyJulius Kühn‐Institut (JKI) – Federal Research Centre for Cultivated PlantsQuedlinburgGermany
| | - Jeremy Pardo
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan
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19
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Burke SV, Ungerer MC, Duvall MR. Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae). BMC PLANT BIOLOGY 2018; 18:152. [PMID: 30075756 PMCID: PMC6091044 DOI: 10.1186/s12870-018-1379-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/30/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae. RESULTS Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6 Ma, with the insert arising at 8.7 Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA. CONCLUSIONS A hypothetical ancestral insert, 17,685 bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808 bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.
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Affiliation(s)
- Sean V. Burke
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861 USA
| | - Mark C. Ungerer
- Division of Biology, Kansas State University, 1717 Claflin Rd, Manhattan, KS 66506-4900 USA
| | - Melvin R. Duvall
- Department of Biological Sciences and Plant Molecular and Bioinformatics Center, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861 USA
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20
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Phylogeny of Maleae (Rosaceae) Based on Multiple Chloroplast Regions: Implications to Genera Circumscription. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7627191. [PMID: 29750171 PMCID: PMC5884435 DOI: 10.1155/2018/7627191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/11/2017] [Accepted: 01/02/2018] [Indexed: 01/15/2023]
Abstract
Maleae consists of economically and ecologically important plants. However, there are considerable disputes on generic circumscription due to the lack of a reliable phylogeny at generic level. In this study, molecular phylogeny of 35 generally accepted genera in Maleae is established using 15 chloroplast regions. Gillenia is the most basal clade of Maleae, followed by Kageneckia + Lindleya, Vauquelinia, and a typical radiation clade, the core Maleae, suggesting that the proposal of four subtribes is reasonable. In the core Maleae including 31 genera, chloroplast gene data support that the four Malus-related genera should better be merged into one genus and the six Sorbus-related genera would be classified into two genera, whereas all Photinia-related genera should be accepted as distinct genera. Although the phylogenetic relationships among the genera in Maleae are much clearer than before, it is still premature to make a formal taxonomic treatment for these genera.
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21
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Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC. Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. AMERICAN JOURNAL OF BOTANY 2018; 105:463-469. [PMID: 29574686 DOI: 10.1002/ajb2.1040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/06/2017] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, 48864, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Michelle Tang
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jill Coombs
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Setareh Mohammadin
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - M Eric Schranz
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - Zhiyong Xiong
- Potato Engineering & Technology Research Center, Inner Mongolia University, Hohhot, China
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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Píchová K, Pažoutová S, Kostovčík M, Chudíčková M, Stodůlková E, Novák P, Flieger M, van der Linde E, Kolařík M. Evolutionary history of ergot with a new infrageneric classification (Hypocreales: Clavicipitaceae: Claviceps). Mol Phylogenet Evol 2018; 123:73-87. [PMID: 29481949 DOI: 10.1016/j.ympev.2018.02.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/12/2017] [Accepted: 02/14/2018] [Indexed: 12/11/2022]
Abstract
The ergot, genus Claviceps, comprises approximately 60 species of specialised ovarial grass parasites famous for the production of food toxins and pharmaceutics. Although the ergot has been known for centuries, its evolution have not been resolved yet. Our approach combining multilocus phylogeny, molecular dating and the study of ecological, morphological and metabolic features shows that Claviceps originated in South America in the Palaeocene on a common ancestor of BEP (subfamilies Bambusoideae, Ehrhartoideae, Pooideae) and PACMAD (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) grasses. Four clades described here as sections diverged during the Paleocene and Eocene. Since Claviceps are parasitic fungi with a close relationship with their host plants, their evolution is influenced by interactions with the new hosts, either by the spread to a new continent or the radiation of the host plants. Three of the sections possess very narrow host ranges and biogeographical distributions and have relatively low toxicity. On the contrary, the section Claviceps, comprising the rye ergot, C. purpurea, is unique in all aspects. Fungi in this section of North American origin have spread all over the world and infect grasses in all subfamilies as well as sedges, and it is the only section synthesising toxic ergopeptines and secalonic acids. The evolutionary success of the Claviceps section members can be explained by high toxin presence, serving as feeding deterrents and playing a role in their protective mutualism with host plants. Closely related taxa Neoclaviceps monostipa and Cepsiclava phalaridis were combined into the genus Aciculosporium.
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Affiliation(s)
- Kamila Píchová
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic; Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12801 Prague, Czech Republic
| | - Sylvie Pažoutová
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Martin Kostovčík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Milada Chudíčková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Eva Stodůlková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Miroslav Flieger
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic
| | - Elna van der Linde
- Biosystematics Division, Plant Protection Research Institute, Agricultural Research Council, Private Bag X134, Pretoria 0121, South Africa
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague, Czech Republic.
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Saarela JM, Burke SV, Wysocki WP, Barrett MD, Clark LG, Craine JM, Peterson PM, Soreng RJ, Vorontsova MS, Duvall MR. A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions. PeerJ 2018; 6:e4299. [PMID: 29416954 PMCID: PMC5798404 DOI: 10.7717/peerj.4299] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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Affiliation(s)
- Jeffery M. Saarela
- Beaty Centre for Species Discovery and Botany Section, Canadian Museum of Nature, Ottawa, ON, Canada
| | - Sean V. Burke
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, Chicago, IL, USA
| | - Matthew D. Barrett
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Lynn G. Clark
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Paul M. Peterson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Robert J. Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Maria S. Vorontsova
- Comparative Plant & Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Melvin R. Duvall
- Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA
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24
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Teisher JK, McKain MR, Schaal BA, Kellogg EA. Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn. ANNALS OF BOTANY 2017; 120. [PMID: 28645142 PMCID: PMC5714200 DOI: 10.1093/aob/mcx058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn - a hygroscopic awn that has been shown to be important in seed germination for some grass species. In this study, the phylogenetic positions of most arundinoid genera were determined using DNA from herbarium specimens, and their placement affects interpretation of this ecologically important trait. METHODS A phylogenetic analysis was conducted on a matrix of full-plastome sequences from 123 species in 107 genera representing all grass subfamilies, with 15 of the 19 genera in subfamily Arundinoideae. Parsimony and maximum likelihood mapping approaches were used to estimate ancestral states for presence of a geniculate lemma awn with a twisted column across Poaceae. Lastly, anatomical characters were examined for former arundinoid taxa using light microscopy and scanning electron microscopy. KEY RESULTS Four genera traditionally included in Arundinoideae fell outside the subfamily in the plastome phylogeny, with the remaining 11 genera forming Arundinoideae sensu stricto . The twisted geniculate awn has originated independently at least five times in the PACMAD grasses, in the subfamilies Panicoideae, Danthonioideae/Chloridoideae and Arundinoideae. Morphological and anatomical characters support the new positions of the misplaced arundinoid genera in the phylogeny, but also highlight convergent and parallel evolution in the grasses. CONCLUSIONS In placing the majority of arundinoid genera in a phylogenetic framework, our study answers one of the last remaining big questions in grass taxonomy while highlighting examples of convergent evolution in an ecologically important trait, the hygroscopic, twisted geniculate awn.
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Affiliation(s)
- J K Teisher
- Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
- For correspondence. E-mail
| | - M R McKain
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - B A Schaal
- Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA
| | - E A Kellogg
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
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25
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Wu Z, Sloan DB, Brown CW, Rosenblueth M, Palmer JD, Ong HC. Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses. Mol Biol Evol 2017; 34:2340-2354. [PMID: 28541477 PMCID: PMC5850859 DOI: 10.1093/molbev/msx170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.
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Affiliation(s)
- Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Colin W. Brown
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX
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26
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Evolutionarily Conserved Alternative Splicing Across Monocots. Genetics 2017; 207:465-480. [PMID: 28839042 DOI: 10.1534/genetics.117.300189] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splice-factor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.
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27
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Pessoa-Filho M, Martins AM, Ferreira ME. Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. BMC Genomics 2017; 18:516. [PMID: 28683832 PMCID: PMC5499013 DOI: 10.1186/s12864-017-3904-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 06/27/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels). RESULTS Whole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya. CONCLUSION Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.
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Affiliation(s)
- Marco Pessoa-Filho
- Embrapa Cerrados, BR 020, Km 18, Planaltina, Brasília, 73310-970 DF Brazil
| | - Alexandre Magalhães Martins
- Laboratório de Genética Vegetal, Embrapa Recursos Genéticos e Biotecnologia, CP 02372 Brasília, Parque Estação Biológica, 70770-900 DF, Brazil
| | - Márcio Elias Ferreira
- Laboratório de Genética Vegetal, Embrapa Recursos Genéticos e Biotecnologia, CP 02372 Brasília, Parque Estação Biológica, 70770-900 DF, Brazil
- Embrapa Labex USA, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Bldg 006 Rm 200, 10300 Ave, Belstville, Baltimore, MD 20705 USA
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28
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Wu Z, Gu C, Tembrock LR, Zhang D, Ge S. Characterization of the whole chloroplast genome of Chikusichloa mutica and its comparison with other rice tribe (Oryzeae) species. PLoS One 2017; 12:e0177553. [PMID: 28542519 PMCID: PMC5443529 DOI: 10.1371/journal.pone.0177553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Chloroplast genomes are a significant genomic resource in plant species and have been used in many research areas. The complete genomic information from wild crop species could supply a valuable genetic reservoir for breeding. Chikusichloa mutica is one of the most important wild distant relatives of cultivated rice. In this study, we sequenced and characterized its complete chloroplast (cp) genome and compared it with other species in the same tribe. The whole cp genome sequence is 136,603 bp in size and exhibits a typical quadripartite structure with large and small single-copy regions (LSC, 82,327 bp; SSC, 12,598 bp) separated by a pair of 20,839-bp inverted repeats (IRA, B). A total of 110 unique genes are annotated, including 76 protein-coding genes, 4 ribosomal RNA genes and 30 tRNA genes. The genome structure, gene order, GC content, and other features are similar to those of other angiosperm cp genomes. When comparing the cp genomes between Oryzinae and Zizaniinae subtribes, the main differences were found between the junction regions and distribution of simple sequence repeats (SSRs). In comparing the two Chikusichloa species, the genomes were only 40 bp different in length and 108 polymorphic sites, including 83 single nucleotide substitutions (SNPs) and 25 insertion-deletions (Indels), were found between the whole cp genomes. The complete cp genome of C. mutica will be an important genetic tool for future breeding programs and understanding the evolution of wild rice relatives.
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Affiliation(s)
- Zhiqiang Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Cuihua Gu
- School of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Luke R. Tembrock
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Dong Zhang
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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29
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Fisher AE, Hasenstab KM, Bell HL, Blaine E, Ingram AL, Columbus JT. Evolutionary history of chloridoid grasses estimated from 122 nuclear loci. Mol Phylogenet Evol 2016; 105:1-14. [DOI: 10.1016/j.ympev.2016.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 10/25/2022]
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30
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Wysocki WP, Burke SV, Swingley WD, Duvall MR. The First Complete Plastid Genome from Joinvilleaceae (J. ascendens; Poales) Shows Unique and Unpredicted Rearrangements. PLoS One 2016; 11:e0163218. [PMID: 27658044 PMCID: PMC5033401 DOI: 10.1371/journal.pone.0163218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/06/2016] [Indexed: 11/19/2022] Open
Abstract
Joinvilleaceae is a family of tropical grass-like monocots that comprises only the genus Joinvillea. Previous studies have placed Joinvilleaceae in close phylogenetic proximity to the well-studied grass family. A full plastome sequence was determined and characterized for J. ascendens. The plastome was sequenced with next generation methods, fully assembled de novo and annotated. The assembly revealed two novel inversions specific to the Joinvilleaceae lineage and at least one novel plastid inversion in the Joinvilleaceae-Poaceae lineage. Two previously documented inversions in the Joinvilleaceae-Poaceae lineage and one previously documented inversion in the Poaceae lineage were also verified. Inversion events were identified visually and verified computationally by simulation mutations. Additionally, the loss and subsequent degradation of the accD gene in order Poales was explored extensively in Poaceae and J. ascendens. The two novel inversions along with changes in gene composition between families better delimited lineages in the Poales. The presence of large inversions and subsequent reversals in this small family suggested a high potential for large-scale rearrangements to occur in plastid genomes.
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Affiliation(s)
- William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, 5454 South Shore Dr., Chicago, IL 60615, United States of America
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
- * E-mail:
| | - Sean V. Burke
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
| | - Wesley D. Swingley
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
| | - Melvin R. Duvall
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
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31
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Schuler ML, Mantegazza O, Weber APM. Engineering C4 photosynthesis into C3 chassis in the synthetic biology age. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:51-65. [PMID: 26945781 DOI: 10.1111/tpj.13155] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 05/21/2023]
Abstract
C4 photosynthetic plants outperform C3 plants in hot and arid climates. By concentrating carbon dioxide around Rubisco C4 plants drastically reduce photorespiration. The frequency with which plants evolved C4 photosynthesis independently challenges researchers to unravel the genetic mechanisms underlying this convergent evolutionary switch. The conversion of C3 crops, such as rice, towards C4 photosynthesis is a long-standing goal. Nevertheless, at the present time, in the age of synthetic biology, this still remains a monumental task, partially because the C4 carbon-concentrating biochemical cycle spans two cell types and thus requires specialized anatomy. Here we review the advances in understanding the molecular basis and the evolution of the C4 trait, advances in the last decades that were driven by systems biology methods. In this review we emphasise essential genetic engineering tools needed to translate our theoretical knowledge into engineering approaches. With our current molecular understanding of the biochemical C4 pathway, we propose a simplified rational engineering model exclusively built with known C4 metabolic components. Moreover, we discuss an alternative approach to the progressing international engineering attempts that would combine targeted mutagenesis and directed evolution.
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Affiliation(s)
- Mara L Schuler
- Institute for Plant Molecular and Developmental Biology, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Otho Mantegazza
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225, Düsseldorf, Germany
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32
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Burke SV, Wysocki WP, Zuloaga FO, Craine JM, Pires JC, Edger PP, Mayfield-Jones D, Clark LG, Kelchner SA, Duvall MR. Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae). BMC PLANT BIOLOGY 2016; 16:140. [PMID: 27316745 PMCID: PMC4912804 DOI: 10.1186/s12870-016-0823-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/27/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. RESULTS 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. CONCLUSIONS The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.
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Affiliation(s)
- Sean V Burke
- Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL, 60115-2861, USA.
| | - William P Wysocki
- Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL, 60115-2861, USA
| | - Fernando O Zuloaga
- Instituto de Botánica Darwinion, Labardén 200, Casilla de Correo 22, B1642HYD, San Isidro, Buenos Aires, Argentina
| | | | - J Chris Pires
- Biological Sciences, University of Missouri, 371b Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA
| | - Dustin Mayfield-Jones
- Donald Danforth Plant Science Center, 975 North Warson Rd, St. Louis, MO, 63132, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, 251 Bessey Hall, Iowa State University, Ames, IA, 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID, 83209-8007, USA
| | - Melvin R Duvall
- Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL, 60115-2861, USA
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33
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Burke SV, Lin CS, Wysocki WP, Clark LG, Duvall MR. Phylogenomics and Plastome Evolution of Tropical Forest Grasses ( Leptaspis, Streptochaeta: Poaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:1993. [PMID: 28083012 PMCID: PMC5186769 DOI: 10.3389/fpls.2016.01993] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/15/2016] [Indexed: 05/08/2023]
Abstract
Studies of complete plastomes have proven informative for our understanding of the molecular evolution and phylogenomics of grasses. In this study, a plastome phylogenomic analysis sampled species from lineages of deeply diverging grasses including Streptochaeta spicata (Anomochlooideae), Leptaspis banksii, and L. zeylanica (both Pharoideae). Plastomes from next generation sequences for three species were assembled by de novo methods. The unambiguously aligned coding and non-coding sequences of the entire plastomes were aligned with those from 43 other grasses and the outgroup Joinvillea ascendens. Outgroup sampling of grasses has previously posed a challenge for plastome phylogenomic studies because of major rearrangements of the plastome. Here, over 81,000 bases of homologous sequence were aligned for phylogenomic and divergence estimation analyses. Rare genomic changes, including persistently long ψycf1 and ψycf2 loci, the loss of the rpoC1 intron, and a 21 base tandem repeat insert in the coding sequence for rps19 defined branch points in the grass phylogeny. Marked differences were seen in the topologies inferred from the complete plastome and two gene matrices, and mean maximum likelihood support values for the former were 10% higher. In the full plastome phylogenomic analyses, the two species of Anomochlooideae were monophyletic. Leptaspis and Pharus were found to be reciprocally monophyletic, with the estimated divergence of two Leptaspis species preceding those of Pharus by over 14 Ma, consistent with historical biogeography. Our estimates for deep divergences among grasses were older than previous such estimates, likely influenced by more complete taxonomic and molecular sampling and the use of recently available or previously unused fossil calibration points.
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Affiliation(s)
- Sean V. Burke
- Department of Biological Sciences, Northern Illinois University, DeKalbIL, USA
- *Correspondence: Sean V. Burke,
| | - Choun-Sea Lin
- Plant Tech Core Unit, Agricultural Biotechnology Research Center, Academia SinicaTaipei, Taiwan
| | - William P. Wysocki
- Department of Biological Sciences, Northern Illinois University, DeKalbIL, USA
| | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, AmesIA, USA
| | - Melvin R. Duvall
- Department of Biological Sciences, Northern Illinois University, DeKalbIL, USA
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