1
|
Schnetz L, Butler RJ, Coates MI, Sansom IJ. The skeletal completeness of the Palaeozoic chondrichthyan fossil record. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231451. [PMID: 38298400 PMCID: PMC10827434 DOI: 10.1098/rsos.231451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
Chondrichthyes (sharks, rays, ratfish and their extinct relatives) originated and diversified in the Palaeozoic but are rarely preserved as articulated or partly articulated remains because of their predominantly cartilaginous endoskeletons. Consequently, their evolutionary history is perceived to be documented predominantly by isolated teeth, scales and fin spines. Here, we aim to capture and analyse the quality of the Palaeozoic chondrichthyan fossil record by using a variation of the skeletal completeness metric, which calculates how complete the skeletons of individuals are compared to estimates of their original entirety. Notably, chondrichthyan completeness is significantly lower than any published vertebrate group: low throughout the Silurian and Permian but peaking in the Devonian and Carboniferous. Scores increase to a range similar to pelycosaurs and parareptiles only when taxa identified solely from isolated teeth, scales and spines are excluded. We argue that environmental influences probably played an important role in chondrichthyan completeness. Sea level significantly negatively correlates with chondrichthyan completeness records and resembles patterns already evident in records of ichthyosaurs, plesiosaurs and sauropodomorphs. Such observed variations in completeness highlight the impact of different sampling biases on the chondrichthyan fossil record and the need to acknowledge these when inferring patterns of chondrichthyan macroevolution.
Collapse
Affiliation(s)
- Lisa Schnetz
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Richard J. Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Michael I. Coates
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637-1508, USA
| | - Ivan J. Sansom
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
2
|
Knowledge Gaps and Missing Links in Understanding Mass Extinctions: Can Mathematical Modeling Help? Phys Life Rev 2022; 41:22-57. [DOI: 10.1016/j.plrev.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
|
3
|
Benson RBJ, Butler R, Close RA, Saupe E, Rabosky DL. Biodiversity across space and time in the fossil record. Curr Biol 2021; 31:R1225-R1236. [PMID: 34637736 DOI: 10.1016/j.cub.2021.07.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.
Collapse
Affiliation(s)
- Roger B J Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Richard Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Erin Saupe
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
4
|
Womack TM, Crampton JS, Hannah MJ, Collins KS. A positive relationship between functional redundancy and temperature in Cenozoic marine ecosystems. Science 2021; 373:1027-1029. [PMID: 34446605 DOI: 10.1126/science.abf8732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/23/2021] [Accepted: 07/28/2021] [Indexed: 11/02/2022]
Abstract
The long-term effects of climate change on biodiversity and biogeographic patterns are uncertain. There are known relationships between geographic area and both the number of species and the number of ecological functional groups-termed the species-area relationship and the functional diversity-area relationship, respectively. We show that there is a positive relationship between the number of species in an area, the number of ecological functional groups, and oceanic temperature in the shallow-marine fossil record of New Zealand over a time span of ~40 million years. One implication of this relationship is that functional redundancy increases with temperature. This reveals a long-lived and persistent association between the spatial structuring of biodiversity, the temperature-dependence of functional redundancy, and shallow-marine biodiversity in mid-latitudes.
Collapse
Affiliation(s)
- T M Womack
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand. .,School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - J S Crampton
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand.,School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - M J Hannah
- School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand.,School of Geography, Environment and Earth Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - K S Collins
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK.,Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| |
Collapse
|
5
|
Close RA, Benson RBJ, Alroy J, Carrano MT, Cleary TJ, Dunne EM, Mannion PD, Uhen MD, Butler RJ. The apparent exponential radiation of Phanerozoic land vertebrates is an artefact of spatial sampling biases. Proc Biol Sci 2020; 287:20200372. [PMID: 32259471 PMCID: PMC7209054 DOI: 10.1098/rspb.2020.0372] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
There is no consensus about how terrestrial biodiversity was assembled through deep time, and in particular whether it has risen exponentially over the Phanerozoic. Using a database of 60 859 fossil occurrences, we show that the spatial extent of the worldwide terrestrial tetrapod fossil record itself expands exponentially through the Phanerozoic. Changes in spatial sampling explain up to 67% of the change in known fossil species counts, and these changes are decoupled from variation in habitable land area that existed through time. Spatial sampling therefore represents a real and profound sampling bias that cannot be explained as redundancy. To address this bias, we estimate terrestrial tetrapod diversity for palaeogeographical regions of approximately equal size. We find that regional-scale diversity was constrained over timespans of tens to hundreds of millions of years, and similar patterns are recovered for major subgroups, such as dinosaurs, mammals and squamates. Although the Cretaceous/Palaeogene mass extinction catalysed an abrupt two- to three-fold increase in regional diversity 66 million years ago, no further increases occurred, and recent levels of regional diversity do not exceed those of the Palaeogene. These results parallel those recovered in analyses of local community-level richness. Taken together, our findings strongly contradict past studies that suggested unbounded diversity increases at local and regional scales over the last 100 million years.
Collapse
Affiliation(s)
- Roger A Close
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger B J Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - John Alroy
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
| | - Matthew T Carrano
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Terri J Cleary
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Emma M Dunne
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London WC1E 6BT, UK
| | - Mark D Uhen
- Department of Atmospheric, Oceanic, and Earth Sciences, George Mason University, Fairfax, VA 22030, USA
| | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
6
|
Mammalian community response to historic volcanic eruptions. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00022-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
7
|
Guinot G, Cavin L. Distinct Responses of Elasmobranchs and Ray-Finned Fishes to Long-Term Global Change. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
8
|
Hobohm C, Janišová M, Steinbauer M, Landi S, Field R, Vanderplank S, Beierkuhnlein C, Grytnes JA, Vetaas OR, Fidelis A, de Nascimento L, Clark VR, Fernández-Palacios JM, Franklin S, Guarino R, Huang J, Krestov P, Ma K, Onipchenko V, Palmer MW, Simon MF, Stolz C, Chiarucci A. Global endemics-area relationships of vascular plants. Perspect Ecol Conserv 2019. [DOI: 10.1016/j.pecon.2019.04.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
9
|
Vavrek MJ. The fragmentation of Pangaea and Mesozoic terrestrial vertebrate biodiversity. Biol Lett 2017; 12:rsbl.2016.0528. [PMID: 27651536 DOI: 10.1098/rsbl.2016.0528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/01/2016] [Indexed: 11/12/2022] Open
Abstract
During the Mesozoic (242-66 million years ago), terrestrial regions underwent a massive shift in their size, position and connectivity. At the beginning of the era, the land masses were joined into a single supercontinent called Pangaea. However, by the end of the Mesozoic, terrestrial regions had become highly fragmented, both owing to the drifting apart of the continental plates and the extremely high sea levels that flooded and divided many regions. How terrestrial biodiversity was affected by this fragmentation and large-scale flooding of the Earth's landmasses is uncertain. Based on a model using the species-area relationship (SAR), terrestrial vertebrate biodiversity would be expected to nearly double through the Mesozoic owing to continental fragmentation, despite a decrease of 24% in total terrestrial area. Previous studies of Mesozoic vertebrates have generally found increases in terrestrial diversity towards the end of the era, although these increases are often attributed to intrinsic or climatic factors. Instead, continental fragmentation over this time may largely explain any observed increase in terrestrial biodiversity. This study demonstrates the importance that non-intrinsic effects can have on the taxonomic success of a group, and the importance of geography to understanding past biodiversity.
Collapse
Affiliation(s)
- Matthew J Vavrek
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6
| |
Collapse
|
10
|
Close RA, Benson RBJ, Upchurch P, Butler RJ. Controlling for the species-area effect supports constrained long-term Mesozoic terrestrial vertebrate diversification. Nat Commun 2017; 8:15381. [PMID: 28530240 PMCID: PMC5458146 DOI: 10.1038/ncomms15381] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 03/23/2017] [Indexed: 11/13/2022] Open
Abstract
Variation in the geographic spread of fossil localities strongly biases inferences about the evolution of biodiversity, due to the ubiquitous scaling of species richness with area. This obscures answers to key questions, such as how tetrapods attained their tremendous extant diversity. Here, we address this problem by applying sampling standardization methods to spatial regions of equal size, within a global Mesozoic-early Palaeogene data set of non-flying terrestrial tetrapods. We recover no significant increase in species richness between the Late Triassic and the Cretaceous/Palaeogene (K/Pg) boundary, strongly supporting bounded diversification in Mesozoic tetrapods. An abrupt tripling of richness in the earliest Palaeogene suggests that this diversity equilibrium was reset following the K/Pg extinction. Spatial heterogeneity in sampling is among the most important biases of fossil data, but has often been overlooked. Our results indicate that controlling for variance in geographic spread in the fossil record significantly impacts inferred patterns of diversity through time. Species richness increases with area sampled, potentially confounding biodiversity patterns from the fossil record. Here, the authors standardize spatial sampling to control for this bias and show that terrestrial vertebrate diversification was bounded during the Mesozoic but that equilibria were reset following the K/Pg extinction.
Collapse
Affiliation(s)
- Roger A Close
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger B J Benson
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - Paul Upchurch
- Department of Earth Sciences, University College London, London WC1E 6BT, UK
| | - Richard J Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| |
Collapse
|
11
|
Near-Stasis in the Long-Term Diversification of Mesozoic Tetrapods. PLoS Biol 2016; 14:e1002359. [PMID: 26807777 PMCID: PMC4726655 DOI: 10.1371/journal.pbio.1002359] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/15/2015] [Indexed: 11/21/2022] Open
Abstract
How did evolution generate the extraordinary diversity of vertebrates on land? Zero species are known prior to ~380 million years ago, and more than 30,000 are present today. An expansionist model suggests this was achieved by large and unbounded increases, leading to substantially greater diversity in the present than at any time in the geological past. This model contrasts starkly with empirical support for constrained diversification in marine animals, suggesting different macroevolutionary processes on land and in the sea. We quantify patterns of vertebrate standing diversity on land during the Mesozoic–early Paleogene interval, applying sample-standardization to a global fossil dataset containing 27,260 occurrences of 4,898 non-marine tetrapod species. Our results show a highly stable pattern of Mesozoic tetrapod diversity at regional and local levels, underpinned by a weakly positive, but near-zero, long-term net diversification rate over 190 million years. Species diversity of non-flying terrestrial tetrapods less than doubled over this interval, despite the origins of exceptionally diverse extant groups within mammals, squamates, amphibians, and dinosaurs. Therefore, although speciose groups of modern tetrapods have Mesozoic origins, rates of Mesozoic diversification inferred from the fossil record are slow compared to those inferred from molecular phylogenies. If high speciation rates did occur in the Mesozoic, then they seem to have been balanced by extinctions among older clades. An apparent 4-fold expansion of species richness after the Cretaceous/Paleogene (K/Pg) boundary deserves further examination in light of potential taxonomic biases, but is consistent with the hypothesis that global environmental disturbances such as mass extinction events can rapidly adjust limits to diversity by restructuring ecosystems, and suggests that the gradualistic evolutionary diversification of tetrapods was punctuated by brief but dramatic episodes of radiation. A large-scale examination of the fossil record reveals slow diversification rates in tetrapods across the 190-million-year Mesozoic era, followed by a possible rapid and abrupt 4-fold increase in species richness after the Cretaceous-Paleogene mass extinction event. Vertebrates invaded the land more than 360 million years ago. Since then, they diversified to more than 30,000 tetrapod species today, including birds, mammals, squamates, and amphibians. The fossil record provides our best window onto diversification across such long spans of time, but is unevenly sampled. Previous studies counted observed families of fossil tetrapods and supported an expansionist model, entailing large and unbounded diversity increases through time. We applied methods that correct for differences in sampling through time and space to a comprehensive species-level database of Mesozoic to early Cenozoic fossil tetrapods. We find strong evidence that tetrapod diversity increased during the Mesozoic, but that the long-term net rate of diversification was low; species richness only doubled or tripled over 190 million years. This is enigmatic because today’s high biodiversity could not have been realised at such a slow rate. Diversification rates must have been much higher during other intervals, or rapid diversification might have been concentrated during brief episodes such as the earliest Cenozoic. Patterns of diversification on geological timescales and their relationships to hypothesised drivers such as ecological opportunity and environmental volatility must receive renewed scrutiny if we are to understand how land vertebrates and other animals attained the high biodiversity seen today.
Collapse
|
12
|
Liu X, Wang Z, Shao W, Ye Z, Zhang J. Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:2022. [PMID: 28101098 PMCID: PMC5209371 DOI: 10.3389/fpls.2016.02022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/19/2016] [Indexed: 05/12/2023]
Abstract
Although, the Abaso section is widely accepted as an independent section, the taxonomic status of Populus mexicana (section Abaso) has not yet been resolved due to the limited availability markers and/or the lack of P. mexicana specimens in previous studies. Thirty-one poplar species that represent six sections of the Populus genus were sampled, and 23 single-copy nuclear DNA and 34 chloroplast fragments were sequenced. The present study obtained two updated phylogenies of Populus. We found that monophyly of the genus Populus is strongly supported by nuclear and plastid gene, which is consistent with previous studies. P. mexicana, diverged first in the nuclear DNA tree, which occupied the basal position, implying that the section Abaso may be the most ancestral lineage in extant populous species. Given that the short branches and low statistical support for the divergence of sections Abaso and Turanga, this observation probably indicated that a rapid radiation evolution following the early split of the genus Populus. In the plastid tree, P. mexicana clustered with modern-day species of section Tacamahaca in the plastid tree. Based on cytoplasmic and single-copy nuclear marker sequences, we hypothesized that chloroplast capture resulted in the inconsistent position of P. mexicana between the phylogenetic trees. Given the first unequivocal records of poplar fossils from the Eocene with similar leaf morphology to the extant P. mexicana and the phylogenetic positions of P. mexicana in our study, we support the hypothesis that the Populus genus originated in North America, which will provide new insights to the development of the origin of Populus species.
Collapse
Affiliation(s)
- Xia Liu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Zhaoshan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China
| | - Wenhao Shao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Research Institute of Subtropical Forestry, Chinese academy of ForestryHangzhou, China
| | - Zhanyang Ye
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry UniversityNanjing, China
- *Correspondence: Jianguo Zhang,
| |
Collapse
|
13
|
Zhang Y, Verhoeff NI, Chen Z, Chen S, Wang M, Zhu Z, Ouwerkerk PBF. Functions of OsDof25 in regulation of OsC4PPDK. PLANT MOLECULAR BIOLOGY 2015; 89:229-42. [PMID: 26337938 PMCID: PMC4579267 DOI: 10.1007/s11103-015-0357-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/31/2015] [Indexed: 05/03/2023]
Abstract
Relative little is known about the functions of the so-called Dof zinc factors in plants. Here we report on the analysis of OsDof25 and show a function in regulation of the important C4 photosynthesis gene, OsC4PPDK in rice. Over-expression of OsDof25 enhanced the expression of OsC4PPDK in transient expression experiments by binding in a specific way to a conserved Dof binding site which was confirmed by yeast and in vitro binding studies. Expression studies using promoter GUS plants as well as qPCR experiments showed that OsDof25 expressed in different tissues including both photosynthetic and non-photosynthetic organs and that expression of OsDof25 was partially overlapping with the OsC4PPDK gene. Conclusive evidence for a role of OsDof25 in regulation of C4PPDK came from loss-of-function and gain-of-function experiments with transgenic rice, which showed that down-regulation or over-expression of OsDof25 correlated with OsC4PPDK expression and that OsDof25 has functions as transcriptional activator.
Collapse
Affiliation(s)
- Y Zhang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
- Graduate School of the Chinese Academy of Sciences, Beijing, 100049, China
| | - N I Verhoeff
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
| | - Z Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - S Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Wusi Rd 247, Fuzhou, 350003, Fujian, China
| | - Mei Wang
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands
- SU BioMedicine/TNO Quality of Life, Zernikedreef 9, P.O. Box 2215, 2301 CE, Leiden, The Netherlands
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - P B F Ouwerkerk
- Department of Molecular and Developmental Genetics, Institute of Biology (IBL), Leiden University, P.O. Box 9505, 2300 RA, Leiden, The Netherlands.
| |
Collapse
|
14
|
Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 2014. [PMID: 25468217 PMCID: PMC4268812 DOI: 10.1186/s13059-014-0506-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Results Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two. Conclusions Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0506-z) contains supplementary material, which is available to authorized users.
Collapse
|
15
|
Badgley C, Smiley TM, Finarelli JA. Great Basin mammal diversity in relation to landscape history. J Mammal 2014. [DOI: 10.1644/13-mamm-s-088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
16
|
Wang J, Källman T, Liu J, Guo Q, Wu Y, Lin K, Lascoux M. Speciation of two desert poplar species triggered by Pleistocene climatic oscillations. Heredity (Edinb) 2014; 112:156-64. [PMID: 24065180 PMCID: PMC3907101 DOI: 10.1038/hdy.2013.87] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 07/07/2013] [Accepted: 07/29/2013] [Indexed: 11/09/2022] Open
Abstract
Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66-1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.
Collapse
Affiliation(s)
- J Wang
- State Key Laboratory of Grassland Ecosystem,
College of Life Science, Lanzhou University, Lanzhou,
China
| | - T Källman
- Department of Ecology and Genetics,
Evolutionary Biology Centre, Uppsala University, Uppsala,
Sweden
| | - J Liu
- State Key Laboratory of Grassland Ecosystem,
College of Life Science, Lanzhou University, Lanzhou,
China
| | - Q Guo
- State Key Laboratory of Grassland Ecosystem,
College of Life Science, Lanzhou University, Lanzhou,
China
| | - Y Wu
- State Key Laboratory of Grassland Ecosystem,
College of Life Science, Lanzhou University, Lanzhou,
China
| | - K Lin
- Laboratory of Evolutionary Genomics, CAS-MPG
Partner Institute for Computational Biology, Chinese Academy of Sciences,
Shanghai, China
- Graduate School of the Chinese Academy of
Sciences, Beijing, China
| | - M Lascoux
- Department of Ecology and Genetics,
Evolutionary Biology Centre, Uppsala University, Uppsala,
Sweden
- Laboratory of Evolutionary Genomics, CAS-MPG
Partner Institute for Computational Biology, Chinese Academy of Sciences,
Shanghai, China
| |
Collapse
|
17
|
Loewen MA, Irmis RB, Sertich JJW, Currie PJ, Sampson SD. Tyrant dinosaur evolution tracks the rise and fall of Late Cretaceous oceans. PLoS One 2013; 8:e79420. [PMID: 24223179 PMCID: PMC3819173 DOI: 10.1371/journal.pone.0079420] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/17/2013] [Indexed: 11/18/2022] Open
Abstract
The Late Cretaceous (∼95–66 million years ago) western North American landmass of Laramidia displayed heightened non-marine vertebrate diversity and intracontinental regionalism relative to other latest Cretaceous Laurasian ecosystems. Processes generating these patterns during this interval remain poorly understood despite their presumed role in the diversification of many clades. Tyrannosauridae, a clade of large-bodied theropod dinosaurs restricted to the Late Cretaceous of Laramidia and Asia, represents an ideal group for investigating Laramidian patterns of evolution. We use new tyrannosaurid discoveries from Utah—including a new taxon which represents the geologically oldest member of the clade—to investigate the evolution and biogeography of Tyrannosauridae. These data suggest a Laramidian origin for Tyrannosauridae, and implicate sea-level related controls in the isolation, diversification, and dispersal of this and many other Late Cretaceous vertebrate clades.
Collapse
Affiliation(s)
- Mark A. Loewen
- Natural History Museum of Utah and Department of Geology & Geophysics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| | - Randall B. Irmis
- Natural History Museum of Utah and Department of Geology & Geophysics, University of Utah, Salt Lake City, Utah, United States of America
| | - Joseph J. W. Sertich
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado, United States of America
| | - Philip J. Currie
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Scott D. Sampson
- Natural History Museum of Utah and Department of Geology & Geophysics, University of Utah, Salt Lake City, Utah, United States of America
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado, United States of America
| |
Collapse
|
18
|
Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0108-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
19
|
Le Loeuff J. Paleobiogeography and biodiversity of Late Maastrichtian dinosaurs: how many dinosaur species went extinct at the Cretaceous-Tertiary boundary? ACTA ACUST UNITED AC 2012. [DOI: 10.2113/gssgfbull.183.6.547] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
The global Late Maastrichtian non-avian dinosaur apparent biodiversity is extensively surveyed for the first time. It amounts to 104 species (including unnamed forms) in 2010. The real biodiversity being obscured by taphonomical biases and the scarcity of the continental fossil record, a species-area relationship is used to estimate it. The results show that several hundreds (between 628 and 1078) non-avian dinosaur species were alive in the Late Maastrichtian, which is almost an order of magnitude above previous estimates. Because of the complex Late Cretaceous palaeobiogeography, discussions about dinosaur extinction should be based on this estimated real global biodiversity, not on the apparent biodiversity of a single area. Given the mean duration of dinosaur genera (7.7 Ma), the presence of so many dinosaur species in the Latest Cretaceous is consistent with the termination of most lineages at the Cretaceous-Tertiary boundary (the Late Maastrichtian sub-stage is 2.8 m.y. long). The Late Maastrichtian dinosaurian biodiversity is therefore consistent with the sudden extinction of the group following the Chicxulub impact.
Collapse
|
20
|
Eick M, Stöhr C. Denitrification by plant roots? New aspects of plant plasma membrane-bound nitrate reductase. PROTOPLASMA 2012; 249:909-918. [PMID: 22160216 DOI: 10.1007/s00709-011-0355-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 11/17/2011] [Indexed: 05/31/2023]
Abstract
A specific form of plasma membrane-bound nitrate reductase in plants is restricted to roots. Two peptides originated from plasma membrane integral proteins isolated from Hordeum vulgare have been assigned as homologues to the subunit NarH of respiratory nitrate reductase of Escherichia coli. Corresponding sequences have been detected for predicted proteins of Populus trichocarpa with high degree of identities for the subunits NarH (75%) and NarG (65%), however, with less accordance for the subunit NarI. These findings coincide with biochemical properties, particularly in regard to the electron donors menadione and succinate. Together with the root-specific and plasma membrane-bound nitrite/NO reductase, nitric oxide is produced under hypoxic conditions in the presence of nitrate. In this context, a possible function in nitrate respiration of plant roots and an involvement of plants in denitrification processes are discussed.
Collapse
Affiliation(s)
- Manuela Eick
- Institut für Botanik, Ernst-Moritz-Arndt-Universität, Grimmer Strasse 88, 17487, Greifswald, Germany
| | | |
Collapse
|
21
|
Lagomarcino AJ, Miller AI. The relationship between genus richness and geographic area in Late Cretaceous marine biotas: epicontinental sea versus open-ocean-facing settings. PLoS One 2012; 7:e40472. [PMID: 22870199 PMCID: PMC3411728 DOI: 10.1371/journal.pone.0040472] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 06/08/2012] [Indexed: 11/19/2022] Open
Abstract
For present-day biotas, close relationships have been documented between the number of species in a given region and the area of the region. To date, however, there have been only limited studies of these relationships in the geologic record, particularly for ancient marine biotas. The recent development of large-scale marine paleontological databases, in conjunction with enhanced geographical mapping tools, now allow for their investigation. At the same time, there has been renewed interest in comparing the environmental and paleobiological properties of two broad-scale marine settings: epicontinental seas, broad expanses of shallow water covering continental areas, and open-ocean-facing settings, shallow shelves and coastlines that rim ocean basins. Recent studies indicate that spatial distributions of taxa and the kinetics of taxon origination and extinction may have differed in these two settings. Against this backdrop, we analyze regional Genus-Area Relationships (GARs) of Late Cretaceous marine invertebrates in epicontinental sea and open-ocean settings using data from the Paleobiology Database. We present a new method for assessing GARs that is particularly appropriate for fossil data when the geographic distribution of these data is patchy and uneven. Results demonstrate clear relationships between genus richness and area for regions worldwide, but indicate that as area increases, genus richness increases more per unit area in epicontinental seas than in open-ocean settings. This difference implies a greater degree of compositional heterogeneity as a function of geographic area in epicontinental sea settings, a finding that is consistent with the emerging understanding of physical differences in the nature of water masses between the two marine settings.
Collapse
Affiliation(s)
- Anne J Lagomarcino
- Department of Geology, University of Cincinnati, Cincinnati, Ohio, United States of America.
| | | |
Collapse
|
22
|
Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, Valè G, Cattivelli L. Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 2012; 50:250-66. [PMID: 21822975 DOI: 10.1007/s12033-011-9443-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population's viability.
Collapse
Affiliation(s)
- Delfina Barabaschi
- CRA, Viticolture Research Centre, Via Casoni 13/A, 31058 Susegana, TV, Italy
| | | | | | | | | | | | | | | |
Collapse
|
23
|
CALEDE JONATHANJM, HOPKINS SAMANTHASB. Intraspecific versus interspecific variation in Miocene Great Basin mylagaulids: implications for systematics and evolutionary history. Zool J Linn Soc 2012. [DOI: 10.1111/j.1096-3642.2011.00765.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
24
|
Benton MJ, Dunhill AM, Lloyd GT, Marx FG. Assessing the quality of the fossil record: insights from vertebrates. ACTA ACUST UNITED AC 2011. [DOI: 10.1144/sp358.6] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractAssessing the quality of the fossil record is notoriously hard, and many recent attempts have used sampling proxies that can be questioned. For example, counts of geological formations and estimated outcrop areas might not be defensible as reliable sampling proxies: geological formations are units of enormously variable dimensions that depend on rock heterogeneity and fossil content (and so are not independent of the fossil record), and outcrop areas are not always proportional to rock exposure, probably a closer indicator of rock availability. It is shown that in many cases formation counts will always correlate with fossil counts, whatever the degree of sampling. It is not clear, in any case, that these proxies provide a good estimate of what is missing in the gap between the known fossil record and reality; rather they largely explore the gap between known and potential fossil records. Further, using simple, single numerical metrics to correct global-scale raw data, or to model sampling-driven patterns may be premature. There are perhaps four approaches to exploring the incompleteness of the fossil record, (1) regional-scale studies of geological completeness; (2) regional- or clade-scale studies of sampling completeness using comprehensive measures of sampling, such as numbers of localities or specimens or fossil quality; (3) phylogenetic and gap-counting methods; and (4) model-based approaches that compare sampling as one of several explanatory variables with measures of environmental change, singly and in combination. We suggest that palaeontologists, like other scientists, should accept that their data are patchy and incomplete, and use appropriate methods to deal with this issue in each analysis. All that matters is whether the data are adequate for a designated study or not. A single answer to the question of whether the fossil record is driven by macroevolution or megabias is unlikely ever to emerge because of temporal, geographical, and taxonomic variance in the data.
Collapse
Affiliation(s)
- Michael J. Benton
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
| | - Alexander M. Dunhill
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
| | - Graeme T. Lloyd
- Department of Palaeontology, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Felix G. Marx
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen's Road, Bristol, BS8 1RJ, UK
- Department of Geology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| |
Collapse
|
25
|
Zhang H, Zhang CQ, Sun ZZ, Yu W, Gu MH, Liu QQ, Li YS. A major locus qS12, located in a duplicated segment of chromosome 12, causes spikelet sterility in an indica-japonica rice hybrid. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1247-56. [PMID: 21792631 DOI: 10.1007/s00122-011-1663-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 07/09/2011] [Indexed: 05/06/2023]
Abstract
Chromosome segment duplications are integral in genome evolution by providing a source for the origin of new genes. In the rice genome, besides an ancient polyploidy event known in the rice common ancestor, it had been identified that there was a special segmental duplication involving chromosomes 11 and 12, but the biological role of this duplication remains unknown. In this study, by using a set of chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) derived from the indica cultivar 9311 and japonica cultivar Nipponbare, a major QTL (qS12) resulting in hybrid male sterility was mapped within ~400 kb region adjacent to the special duplicated segment on the short arm of chromosome 12. Compared to the japonica cultivar Nipponbare, the two sides of the qS12 candidate region were inverted in the indica cultivar 9311. Among 47 of the 111 rice genotypes evaluated by molecular markers, the inverted sides were detected, and found completely homologous to indica cultivar 9311. These results suggested that the two inverted sides protect the sequence in the qS12 regions from recombination. On the short-arm of chromosome 12, two QTLs S-e and S25, in addition to qS12, were previously detected as a distinct segregation distortion and pollen semi-sterility loci. We propose these three hybrid sterility loci are the same locus, and the duplicated segment on chromosome 12 may play a prominent role in diversification, i.e., sub-speciation of cultivated rice.
Collapse
Affiliation(s)
- Hua Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory of Plant Developmental Biology of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | | | | | | | | | | | | |
Collapse
|
26
|
Raia P, Carotenuto F, Eronen JT, Fortelius M. Longer in the tooth, shorter in the record? The evolutionary correlates of hypsodonty in Neogene ruminants. Proc Biol Sci 2011; 278:3474-81. [PMID: 21471111 DOI: 10.1098/rspb.2011.0273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The acquisition of hypsodont molars is often regarded as a key innovation in the history of ruminant ungulates. Hypsodont ruminants diversified rapidly during the later Neogene, circa 15-2 Myr ago, and came to dominate the ruminant fossil record in terms of species diversity. Here we show that hypsodont clades had higher speciation and diversification rates than other clades. Hypsodont species had, on average, shorter stratigraphic durations, smaller range size and lower occupancy than non-hypsodont species. Within hypsodont clades, some species were very common and acquired large geographical ranges, whereas others were quite rare and geographically limited. We argue that hypsodont clades diversified in an adaptive radiation-like fashion, with species often splitting cladogenetically while still in the expansive phase of their occupancy history.
Collapse
Affiliation(s)
- P Raia
- Dipartimento di Scienze della Terra, Università degli studi Federico II, Largo San Marcellino 10, 80138 Napoli, Italy.
| | | | | | | |
Collapse
|
27
|
White EP, Ernest SKM, Adler PB, Hurlbert AH, Lyons SK. Integrating spatial and temporal approaches to understanding species richness. Philos Trans R Soc Lond B Biol Sci 2011; 365:3633-43. [PMID: 20980312 DOI: 10.1098/rstb.2010.0280] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding species richness patterns represents one of the most fundamental problems in ecology. Most research in this area has focused on spatial gradients of species richness, with a smaller area of emphasis dedicated to understanding the temporal dynamics of richness. However, few attempts have been made to understand the linkages between the spatial and temporal patterns related to richness. Here, we argue that spatial and temporal richness patterns and the processes that drive them are inherently linked, and that our understanding of richness will be substantially improved by considering them simultaneously. The species-time-area relationship provides a case in point: successful description of the empirical spatio-temporal pattern led to a rapid development and testing of new theories. Other areas of research on species richness could also benefit from an explicitly spatio-temporal approach, and we suggest future directions for understanding the processes common to these two traditionally isolated fields of research.
Collapse
Affiliation(s)
- Ethan P White
- Department of Biology, The Ecology Center, Utah State University, Logan, UT, USA.
| | | | | | | | | |
Collapse
|
28
|
Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G. Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.). BMC Genomics 2010; 11:656. [PMID: 21106060 PMCID: PMC3091774 DOI: 10.1186/1471-2164-11-656] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Accepted: 11/24/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genetic populations provide the basis for a wide range of genetic and genomic studies and have been widely used in genetic mapping, gene discovery and genomics-assisted breeding. Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics. RESULTS In this study, a wide population consisting of 128 CSSLs was developed, derived from the crossing and back-crossing of two sequenced rice cultivars: 9311, an elite indica cultivar as the recipient and Nipponbare, a japonica cultivar as the donor. First, a physical map of the 128 CSSLs was constructed on the basis of estimates of the lengths and locations of the substituted chromosome segments using 254 PCR-based molecular markers. From this map, the total size of the 142 substituted segments in the population was 882.2 Mb, was 2.37 times that of the rice genome. Second, every CSSL underwent high-throughput genotyping by whole-genome re-sequencing with a 0.13× genome sequence, and an ultrahigh-quality physical map was constructed. This sequencing-based physical map indicated that 117 new segments were detected; almost all were shorter than 3 Mb and were not apparent in the molecular marker map. Furthermore, relative to the molecular marker-based map, the sequencing-based map yielded more precise recombination breakpoint determination and greater accuracy of the lengths of the substituted segments, and provided more accurate background information. Third, using the 128 CSSLs combined with the bin-map converted from the sequencing-based physical map, a multiple linear regression QTL analysis mapped nine QTLs, which explained 89.50% of the phenotypic variance for culm length. A large-effect QTL was located in a 791,655 bp region that contained the rice 'green revolution' gene. CONCLUSIONS The present results demonstrated that high throughput genotyped CSSLs combine the advantages of an ultrahigh-quality physical map with high mapping accuracy, thus being of great potential value for gene discovery and genetic mapping. These CSSLs may provide powerful tools for future whole genome large-scale gene discovery in rice and offer foundations enabling the development of superior rice varieties.
Collapse
Affiliation(s)
- Jianjun Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Qiang Zhao
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Peina Du
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Baohe Wang
- Lixiahe Region Agricultural Research Institute of Jiangsu, 225007, Yangzhou, PR China
| | - Qi Feng
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, PR China
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, 88 Daxue Road, Yangzhou 225009, PR China
| |
Collapse
|
29
|
Philippe R, Courtois B, McNally KL, Mournet P, El-Malki R, Le Paslier MC, Fabre D, Billot C, Brunel D, Glaszmann JC, This D. Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:769-787. [PMID: 20454772 DOI: 10.1007/s00122-010-1348-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 04/19/2010] [Indexed: 05/29/2023]
Abstract
Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.
Collapse
Affiliation(s)
- Romain Philippe
- CIRAD, UMR Développement et Amélioration des Plantes, TA-A 96/03, 34398, Montpellier, France.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Umate P, Tuteja R, Tuteja N. Genome-wide analysis of helicase gene family from rice and Arabidopsis: a comparison with yeast and human. PLANT MOLECULAR BIOLOGY 2010; 73:449-65. [PMID: 20383562 DOI: 10.1007/s11103-010-9632-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 03/18/2010] [Indexed: 05/04/2023]
Abstract
Helicases are motor proteins which can catalyze the unwinding of stable RNA or DNA duplex utilizing mainly ATP as source of energy. In this study we have identified complete sets of helicases from rice and Arabidopsis. The helicase gene family in rice and Arabidopsis contains 115 and 113 genes respectively. These helicases were validated based on their annotations and supported with organization of conserved helicase signature motifs. We have also identified homologs of 64 rice RNA and DNA helicases in Arabidopsis, yeast and human. We explored Arabidopsis oligonucleotide array data to gain functional insights into the transcriptome of helicase family members under ten different stress conditions. Our results revealed that expression of helicase genes is profoundly regulated under various stress conditions. The helicases identified in this study lay a foundation for the in depth characterization of each helicase type.
Collapse
Affiliation(s)
- Pavan Umate
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | |
Collapse
|
31
|
|
32
|
BUTLER RICHARDJ, BARRETT PAULM, PENN MALCOLMG, KENRICK PAUL. Testing coevolutionary hypotheses over geological timescales: interactions between Cretaceous dinosaurs and plants. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01401.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
33
|
Carrasco MA, Barnosky AD, Graham RW. Quantifying the extent of North American mammal extinction relative to the pre-anthropogenic baseline. PLoS One 2009; 4:e8331. [PMID: 20016820 PMCID: PMC2789409 DOI: 10.1371/journal.pone.0008331] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 11/19/2009] [Indexed: 11/19/2022] Open
Abstract
Earth has experienced five major extinction events in the past 450 million years. Many scientists suggest we are now witnessing a sixth, driven by human impacts. However, it has been difficult to quantify the real extent of the current extinction episode, either for a given taxonomic group at the continental scale or for the worldwide biota, largely because comparisons of pre-anthropogenic and anthropogenic biodiversity baselines have been unavailable. Here, we compute those baselines for mammals of temperate North America, using a sampling-standardized rich fossil record to reconstruct species-area relationships for a series of time slices ranging from 30 million to 500 years ago. We show that shortly after humans first arrived in North America, mammalian diversity dropped to become at least 15%–42% too low compared to the “normal” diversity baseline that had existed for millions of years. While the Holocene reduction in North American mammal diversity has long been recognized qualitatively, our results provide a quantitative measure that clarifies how significant the diversity reduction actually was. If mass extinctions are defined as loss of at least 75% of species on a global scale, our data suggest that North American mammals had already progressed one-fifth to more than halfway (depending on biogeographic province) towards that benchmark, even before industrialized society began to affect them. Data currently are not available to make similar quantitative estimates for other continents, but qualitative declines in Holocene mammal diversity are also widely recognized in South America, Eurasia, and Australia. Extending our methodology to mammals in these areas, as well as to other taxa where possible, would provide a reasonable way to assess the magnitude of global extinction, the biodiversity impact of extinctions of currently threatened species, and the efficacy of conservation efforts into the future.
Collapse
Affiliation(s)
- Marc A Carrasco
- Department of Integrative Biology, University of California, Berkeley, California, USA.
| | | | | |
Collapse
|
34
|
Edger PP, Pires JC. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res 2009; 17:699-717. [PMID: 19802709 DOI: 10.1007/s10577-009-9055-9] [Citation(s) in RCA: 246] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Whole genome duplications (WGDs) followed by diploidization, which includes gene loss, have been an important recurrent process in the evolution of higher eukaryotes. Gene retention is biased to specific functional gene categories during diploidization. Dosage-sensitive genes, which include transcription factors, are significantly over-retained following WGDs. By contrast, these same functional gene categories exhibit lower retention rates following smaller scale duplications (e.g., local and tandem duplicates, segmental duplicates, aneuploidy). In light of these recent observations, we review current theories that address the fate of nuclear genes following duplication events (i.e., Gain of Function Hypothesis, Subfunctionalization Hypothesis, Increased Gene Dosage Hypothesis, Functional Buffering Model, and the Gene Balance Hypothesis). We broadly review different mechanisms of dosage-compensation that have evolved to alleviate harmful dosage-imbalances. In addition, we examine a recently proposed extension of the Gene Balance Hypothesis to explain the shared single copy status for a specific functional class of genes across the flowering plants. We speculate that the preferential retention of dosage-sensitive genes (e.g., regulatory genes such as transcription factors) and gene loss following WGDs has played a significant role in the development of morphological complexity in eukaryotes and facilitating speciation, respectively. Lastly, we will review recent findings that suggest polyploid lineages had increased rates of survival and speciation following mass extinction events, including the Cretaceous-Tertiary (KT) extinction.
Collapse
Affiliation(s)
- Patrick P Edger
- 371 Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | | |
Collapse
|
35
|
A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice. Genetics 2009; 183:1235-47. [PMID: 19797045 DOI: 10.1534/genetics.109.107409] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 + R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.
Collapse
|
36
|
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B. High-throughput genotyping by whole-genome resequencing. Genome Res 2009; 19:1068-76. [PMID: 19420380 DOI: 10.1101/gr.089516.108] [Citation(s) in RCA: 511] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
Collapse
Affiliation(s)
- Xuehui Huang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Throude M, Bolot S, Bosio M, Pont C, Sarda X, Quraishi UM, Bourgis F, Lessard P, Rogowsky P, Ghesquiere A, Murigneux A, Charmet G, Perez P, Salse J. Structure and expression analysis of rice paleo duplications. Nucleic Acids Res 2009; 37:1248-59. [PMID: 19136467 PMCID: PMC2651813 DOI: 10.1093/nar/gkn1048] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution.
Collapse
Affiliation(s)
- Mickael Throude
- UMR 1095 INRA/UBP, Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Domaine de Crouelle, 234, 63100 Clermont Ferrand, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Would species richness estimators change the observed species area relationship? ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2009. [DOI: 10.1016/j.actao.2008.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
39
|
Paterson AH, Bowers JE, Feltus FA, Tang H, Lin L, Wang X. Comparative genomics of grasses promises a bountiful harvest. PLANT PHYSIOLOGY 2009; 149:125-31. [PMID: 19126703 PMCID: PMC2613718 DOI: 10.1104/pp.108.129262] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 11/05/2008] [Indexed: 05/18/2023]
Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
| | | | | | | | | | | |
Collapse
|
40
|
Huang X, Lu G, Zhao Q, Liu X, Han B. Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. PLANT PHYSIOLOGY 2008; 148:25-40. [PMID: 18650402 PMCID: PMC2528094 DOI: 10.1104/pp.108.121491] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Accepted: 07/17/2008] [Indexed: 05/18/2023]
Abstract
Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.
Collapse
Affiliation(s)
- Xuehui Huang
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China
| | | | | | | | | |
Collapse
|
41
|
Abstract
Motivation: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known. Results: In this article we solve this longstanding open problem by providing the first exact and efficient solution. We also demonstrate the improvement offered by our algorithm over the best heuristic approaches, by applying it to several simulated as well as empirical datasets. Contact:oeulenst@cs.iastate.edu
Collapse
Affiliation(s)
- Mukul S Bansal
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | | |
Collapse
|
42
|
The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica. Funct Integr Genomics 2008; 9:97-108. [PMID: 18633654 DOI: 10.1007/s10142-008-0091-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2008] [Revised: 06/08/2008] [Accepted: 06/08/2008] [Indexed: 10/21/2022]
Abstract
Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.
Collapse
|
43
|
Chung MC, Lee YI, Cheng YY, Chou YJ, Lu CF. Chromosomal polymorphism of ribosomal genes in the genus Oryza. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:745-53. [PMID: 18214422 PMCID: PMC2271086 DOI: 10.1007/s00122-007-0705-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 12/20/2007] [Indexed: 05/04/2023]
Abstract
The genes encoding for 18S-5.8S-28S ribosomal RNA (rDNA) are both conserved and diversified. We used rDNA as probe in the fluorescent in situ hybridization (rDNA-FISH) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species. These included cultivated and wild species of rice, and four of them are tetraploids. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci varies from one to eight among Oryza species. The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza. The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions. In this study, we report two genome specific rDNA loci in the genus Oryza. One is specific to the BB genome, which was localized at the end of the short arm of chromosome 4. Another may be specific to the CC genome, which was localized in the proximal region of the short arm of chromosome 5. A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O. grandiglumis by rDNA-FISH. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution. The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed.
Collapse
MESH Headings
- Chromosomes, Plant/genetics
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer
- Genome, Plant
- In Situ Hybridization, Fluorescence
- Oryza/genetics
- Polymorphism, Genetic
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 5S/genetics
Collapse
Affiliation(s)
- Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan, Republic of China.
| | | | | | | | | |
Collapse
|
44
|
Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. THE PLANT CELL 2008; 20:11-24. [PMID: 18178768 PMCID: PMC2254919 DOI: 10.1105/tpc.107.056309] [Citation(s) in RCA: 258] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/21/2007] [Accepted: 12/12/2007] [Indexed: 05/17/2023]
Abstract
The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
Collapse
Affiliation(s)
- Jérôme Salse
- Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Agalou A, Purwantomo S, Overnäs E, Johannesson H, Zhu X, Estiati A, de Kam RJ, Engström P, Slamet-Loedin IH, Zhu Z, Wang M, Xiong L, Meijer AH, Ouwerkerk PBF. A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. PLANT MOLECULAR BIOLOGY 2008; 66:87-103. [PMID: 17999151 DOI: 10.1007/s11103-007-9255-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2007] [Accepted: 10/25/2007] [Indexed: 05/20/2023]
Abstract
The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.
Collapse
Affiliation(s)
- Adamantia Agalou
- Institute of Biology, Clusius Laboratory, Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Construction of a bacterial artificial chromosome (BAC) library of common wild rice (Oryza rufipogon Griff.) for map-based cloning of genes selected during the domestication of rice. Biotechnol Lett 2007; 30:555-61. [DOI: 10.1007/s10529-007-9558-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 09/20/2007] [Accepted: 09/21/2007] [Indexed: 10/22/2022]
|
47
|
Yamamoto E, Takashi T, Morinaka Y, Lin S, Kitano H, Matsuoka M, Ashikari M. Interaction of two recessive genes, hbd2 and hbd3, induces hybrid breakdown in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:187-94. [PMID: 17487470 DOI: 10.1007/s00122-007-0554-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Accepted: 04/10/2007] [Indexed: 05/09/2023]
Abstract
Reproductive barriers are important for the maintenance of species identity. We discovered a reproductive barrier via hybrid breakdown among the progeny of a cross between the japonica rice cultivar Koshihikari and the indica rice cultivar Habataki. Genetic analysis indicated that the hybrid breakdown is regulated by the interaction of two recessive genes: hbd2 in Habataki and hbd3 in Koshihikari. Linkage mapping showed that hbd2 is located near the 100 cM region of chromosome 2 in Habataki, whereas hbd3 is located near the 60 cM region of chromosome 11 in Koshihikari. Construction of nearly isogenic lines for hbd2 and Hbd3 (NIL-hbd2 and NIL-Hbd3), as well as a pyramiding line (NIL-hbd2 + Hbd3), confirmed that the hybrid breakdown is induced by the interaction of these two recessive genes. Our results indicate that these genes are novel for the induction of hybrid breakdown in rice.
Collapse
Affiliation(s)
- Eiji Yamamoto
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan
| | | | | | | | | | | | | |
Collapse
|
48
|
McSteen P, Malcomber S, Skirpan A, Lunde C, Wu X, Kellogg E, Hake S. barren inflorescence2 Encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. PLANT PHYSIOLOGY 2007; 144:1000-11. [PMID: 17449648 PMCID: PMC1914211 DOI: 10.1104/pp.107.098558] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Organogenesis in plants is controlled by meristems. Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. Maize (Zea mays) and rice (Oryza sativa) have additional types of axillary meristems in the inflorescence compared to Arabidopsis (Arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. Previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed that bif2 plays a key role in axillary meristem and lateral primordia initiation in the inflorescence. In this article, we cloned bif2 by transposon tagging. Isolation of bif2-like genes from seven other grasses, along with phylogenetic analysis, showed that bif2 is a co-ortholog of PINOID (PID), which regulates auxin transport in Arabidopsis. Expression analysis showed that bif2 is expressed in all axillary meristems and lateral primordia during inflorescence and vegetative development in maize and rice. Further phenotypic analysis of bif2 mutants in maize illustrates additional roles of bif2 during vegetative development. We propose that bif2/PID sequence and expression are conserved between grasses and Arabidopsis, attesting to the important role they play in development. We provide further support that bif2, and by analogy PID, is required for initiation of both axillary meristems and lateral primordia.
Collapse
Affiliation(s)
- Paula McSteen
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
| | | | | | | | | | | | | |
Collapse
|
49
|
Weng C, Hooghiemstra H, Duivenvoorden JF. Response of pollen diversity to the climate-driven altitudinal shift of vegetation in the Colombian Andes. Philos Trans R Soc Lond B Biol Sci 2007; 362:253-62. [PMID: 17255034 PMCID: PMC2311429 DOI: 10.1098/rstb.2006.1985] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Change in diversity of fossil pollen through time is used as a surrogate for biodiversity history. However, there have been few studies to explore the sensitivity of the measured pollen diversity to vegetation changes and the relationship between pollen diversity and plant diversity. This paper presents results of a study to assess the relationship between pollen diversity and relative abundance of pollen from different altitudinal vegetation belts (subandean forest, Andean forest, subparamo and grassparamo) in three records from the tropical Andes in Colombia. The results indicated that plant diversity in the vegetation declined with altitude and pollen diversity is positively correlated to the abundance of pollen from lower altitude vegetation belts and negatively correlated to that from the grassparamo. These results, therefore, suggest that pollen diversity coarsely reflects the diversity of the surrounding vegetation. Using this interpretation, we were able to predict changes in plant diversity over the past 430000 years in the Colombian Andes. Results indicated that under warmer climatic conditions, more species-diverse vegetation of low elevation moved upslope to contribute more pollen diversity to the study sites, and under colder conditions, species-poor grassparamo moved downslope and observed pollen diversity was lower. This study concludes that fossil pollen diversity may provide an important proxy to reconstruct the temporal changes in plant diversity.
Collapse
Affiliation(s)
- Chengyu Weng
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands.
| | | | | |
Collapse
|
50
|
Pareek A, Singh A, Kumar M, Kushwaha HR, Lynn AM, Singla-Pareek SL. Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis. PLANT PHYSIOLOGY 2006; 142:380-97. [PMID: 16891544 PMCID: PMC1586034 DOI: 10.1104/pp.106.086371] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants.
Collapse
Affiliation(s)
- Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | | | | | | | | | | |
Collapse
|