scholarly journals The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenchuang He ◽  
Caijin Chen ◽  
Kunli Xiang ◽  
Jie Wang ◽  
Ping Zheng ◽  
...  
Keyword(s):  
Wild Rice ◽  
De Novo ◽  
Oryza Rufipogon ◽  
Molecular Dating ◽  
Data Set ◽  
Biogeographic History ◽  
Plastid Genomes ◽  
History Of ◽  
Genetic Clusters ◽  
Rice Domestication

The plastid is an essential organelle in autotrophic plant cells, descending from free-living cyanobacteria and acquired by early eukaryotic cells through endosymbiosis roughly one billion years ago. It contained a streamlined genome (plastome) that is uniparentally inherited and non-recombinant, which makes it an ideal tool for resolving the origin and diversity of plant species and populations. In the present study, a large dataset was amassed by de novo assembling plastomes from 295 common wild rice (Oryza rufipogon Griff.) and 1135 Asian cultivated rice (Oryza sativa L.) accessions, supplemented with 34 plastomes from other Oryza species. From this dataset, the phylogenetic relationships and biogeographic history of O. rufipogon and O. sativa were reconstructed. Our results revealed two major maternal lineages across the two species, which further diverged into nine well supported genetic clusters. Among them, the Or-wj-I/II/III and Or-wi-I/II genetic clusters were shared with cultivated (percentage for each cluster ranging 54.9%∼99.3%) and wild rice accessions. Molecular dating, phylogeographic analyses and reconstruction of population historical dynamics indicated an earlier origin of the Or-wj-I/II genetic clusters from East Asian with at least two population expansions, and later origins of other genetic clusters from multiple regions with one or more population expansions. These results supported a single origin of japonica rice (mainly in Or-wj-I/II) and multiple origins of indica rice (in all five clusters) for the history of rice domestication. The massive plastomic data set presented here provides an important resource for understanding the history and evolution of rice domestication as well as a genomic resources for use in future breeding and conservation efforts.

scholarly journals Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae)

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Kole F. Adelalu ◽  
Xu Zhang ◽  
Xiaojian Qu ◽  
Jacob B. Landis ◽  
Jun Shen ◽  
...  
Keyword(s):  
North America ◽  
East Asia ◽  
Potential Effect ◽  
Molecular Dating ◽  
Disjunct Distribution ◽  
Land Bridge ◽  
Biogeographic History ◽  
Extant Species ◽  
History Of ◽  
Phylogenomic Analyses

Investigating the biogeographical disjunction of East Asian and North American flora is key to understanding the formation and dynamics of biodiversity in the Northern Hemisphere. The small Cupressaceae genus Thuja, comprising five species, exhibits a typical disjunct distribution in East Asia and North America. Owing to obscure relationships, the biogeographical history of the genus remains controversial. Here, complete plastomes were employed to investigate the plastome evolution, phylogenetic relationships, and biogeographic history of Thuja. All plastomes of Thuja share the same gene content arranged in the same order. The loss of an IR was evident in all Thuja plastomes, and the B-arrangement as previously recognized was detected. Phylogenomic analyses resolved two sister pairs, T. standishii-T. koraiensis and T. occidentalis-T. sutchuenensis, with T. plicata sister to T. occidentalis-T. sutchuenensis. Molecular dating and biogeographic results suggest the diversification of Thuja occurred in the Middle Miocene, and the ancestral area of extant species was located in northern East Asia. Incorporating the fossil record, we inferred that Thuja likely originated from the high-latitude areas of North America in the Paleocene with a second diversification center in northern East Asia. The current geographical distribution of Thuja was likely shaped by dispersal events attributed to the Bering Land Bridge in the Miocene and subsequent vicariance events accompanying climate cooling. The potential effect of extinction may have profound influence on the biogeographical history of Thuja.

scholarly journals The double odyssey of Madagascan polystome flatworms leads to new insights on the origins of their amphibian hosts

2009 ◽  
Vol 276 (1662) ◽  
pp. 1575-1583 ◽  
Author(s):  
Olivier Verneau ◽  
Louis H Du Preez ◽  
Véronique Laurent ◽  
Liliane Raharivololoniaina ◽  
Frank Glaw ◽  
...  
Keyword(s):  
Molecular Dating ◽  
Phylogenetic Position ◽  
Late Mesozoic ◽  
Biogeographic History ◽  
On This Island ◽  
The Family ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Recent Origin ◽  
High Species Richness

Polystomatid flatworms are parasites of high host specificity, which mainly infect amphibian hosts. Only one polystome species has so far been recorded from Madagascar despite the high species richness and endemicity of amphibians on this island. Out of the 86 screened Malagasy frog species, we recovered polystomes from 25 in the families Ptychadenidae and Mantellidae. Molecular phylogenetic analysis uncovered an unexpected diversity of polystome species belonging to two separate clades: one forming a lineage within the genus Metapolystoma , with one species in Ptychadena and several species in the mantellid host genera Aglyptodactylus and Boophis ; and the second corresponding to an undescribed genus that was found in the species of the subfamily Mantellinae in the family Mantellidae. The phylogenetic position of the undescribed genus along with molecular dating suggests that it may have colonized Madagascar in the Late Mesozoic or Early Cainozoic. By contrast, the more recent origin of Metapolystoma in Madagascar at ca 14–2 Myr ago strongly suggests that the ancestors of Ptychadena mascareniensis colonized Madagascar naturally by overseas dispersal, carrying their Metapolystoma parasites. Our findings provide a striking example of how parasite data can supply novel insights into the biogeographic history of their hosts.

Eritreo-Arabian Affinities of the Socotran Flora as Revealed from the Molecular Phylogeny of Aerva (Amaranthaceae)

2006 ◽  
Vol 31 (3) ◽  
pp. 560-570 ◽  
Author(s):  
Mike Thiv ◽  
Mats Thulin ◽  
Norbert Kilian ◽  
H. Peter Linder
Keyword(s):  
Indian Ocean ◽  
Sequence Data ◽  
Plastid Dna ◽  
Molecular Dating ◽  
Tropical Asia ◽  
Biogeographic Patterns ◽  
Dna Sequence Data ◽  
Biogeographic History ◽  
History Of ◽  
Taxonomic Groups

We investigated the colonization of the Indian Ocean archipelago of Socotra through phylogenetic analysis of Aerva (Amaranthaceae) based on nuclear and plastid DNA sequence data. The biogeographic history of the genus was tracked using ancestral area reconstructions and molecular dating. Three independent colonization lineages from the Eritreo-Arabian subregion of the Sudano-Zambesian Region were revealed: one endemic clade comprising Aerva revoluta / A. microphylla and once within A. lanata and A. javanica. Our results provide further support for the dominance of Eritreo-Arabian affinities in the flora of Socotra, in contrast to more rare affinities to Madagascar, the Mascarenes, southern Africa, and tropical Asia. Our data point towards colonization via dispersal, rather than a vicariance origin of the island elements. The overall biogeographic patterns of Aerva show only limited concordance with other taxonomic groups distributed on Indian Ocean islands.

scholarly journals Pattern and Timing of Diversification in the African Freshwater Fish Genus Distichodus (Characiformes: Distichodontidae)

2019 ◽  
Author(s):  
Jairo Arroyave ◽  
John S. S. Denton ◽  
Melanie L. J. Stiassny
Keyword(s):  
Freshwater Fish ◽  
Sequence Data ◽  
Time Estimation ◽  
Geographic Range ◽  
Molecular Dating ◽  
Congo Basin ◽  
Similar Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
History Of

Abstract Background: Distichodus, the type genus of the endemic African characiform family Distichodontidae, is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. Results: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group.Conclusions: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment ever conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies might be a consequence of deep coalescence and recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting acomplex scenario for the assemblage of Africa’s continental ichthyofaunal communities. Keywords: Distichodontidae, Distichodus, Congo Basin, molecular phylogeny, African fishes, geographic range evolution, molecular dating.

scholarly journals SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

2020 ◽  
Author(s):  
Wei Li ◽  
Kui Li ◽  
Ying Huang ◽  
Cong Shi ◽  
Wu-Shu Hu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Wild Rice ◽  
De Novo ◽  
Rice Genome ◽  
Gene Families ◽  
Oryza Rufipogon ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Cultivated Rice ◽  
Reproductive Process

AbstractAsian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10× and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

scholarly journals Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

2018 ◽  
Vol 8 (23) ◽  
pp. 12056-12065
Author(s):  
Salinda Sandamal ◽  
Asanka Tennakoon ◽  
Qing-Lin Meng ◽  
Buddhi Marambe ◽  
Disna Ratnasekera ◽  
...  
Keyword(s):  
Population Genetics ◽  
Sri Lanka ◽  
Wild Rice ◽  
Evolutionary History ◽  
Oryza Rufipogon ◽  
Wild Rice Species ◽  
History Of

scholarly journals Identification and genetic analysis of qCL1.2, a novel allele of the “green revolution” gene SD1 from wild rice (Oryza rufipogon) that enhances plant height

2020 ◽  
Author(s):  
Lizhen Zhang ◽  
Jingfen Huang ◽  
Yanyan Wang ◽  
Rui Xu ◽  
Ziyi Yang ◽  
...  
Keyword(s):  
Plant Height ◽  
Wild Rice ◽  
Green Revolution ◽  
Oryza Rufipogon ◽  
Gibberellin Biosynthesis ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Wild Allele ◽  
Novel Allele ◽  
Rice Domestication

Abstract Background: The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.Results: We identified a PH-related quantitative trait locus, qCL1.2, from wild rice using a set of chromosome segment substitution lines. qCL1.2 encodes a novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2,822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increases understanding of the rice SD1 gene and provides additional evidence of this gene’s selection during rice domestication.Conclusions: Our findings provide evidence that SD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

scholarly journals Identification and genetic analysis of qCL1.2 , a novel allele of the “green revolution” gene SD1 from wild rice ( Oryza rufipogon ) that enhances plant height

2020 ◽  
Author(s):  
Lizhen Zhang ◽  
Jingfen Huang ◽  
Yanyan Wang ◽  
Rui Xu ◽  
Ziyi Yang ◽  
...  
Keyword(s):  
Plant Height ◽  
Wild Rice ◽  
Green Revolution ◽  
Oryza Rufipogon ◽  
Gibberellin Biosynthesis ◽  
Nucleotide Polymorphisms ◽  
Network Analyses ◽  
Wild Allele ◽  
Novel Allele ◽  
Rice Domestication

Abstract Background: The exploitation of novel alleles from wild rice that were lost during rice cultivation could be very important for rice breeding and evolutionary studies. Plant height (PH) was a target of artificial selection during rice domestication and is still a target of modern breeding. The “green revolution” gene semi-dwarf 1 (SD1) were well documented and used in the past decades, allele from wild rice could provide new insights into the functions and evolution of this gene.Results: We identified a PH-related quantitative trait locus, qCL1.2, from wild rice using a set of chromosome segment substitution lines. qCL1.2 encodes a novel allele of SD1 gene. The wild allele of SD1 is a dominant locus that can significantly promote rice internode length by regulating the expression levels of genes involved in gibberellin biosynthesis and signal transduction. Nucleotide diversity and haplotype network analyses of the SD1 gene were performed using 2,822 rice landraces. Two previously reported functional nucleotide polymorphisms clearly differentiated japonica and indica rice; however, they were not associated with PH selection. Other new functional nucleotide polymorphisms in the coding, but not promoter, regions were involved in PH selection during rice domestication. Our study increases understanding of the rice SD1 gene and provides additional evidence of this gene’s selection during rice domestication.Conclusions: Our findings provide evidence that SD1 gene from wild rice enhances plant height and new functional nucleotide polymorphisms of this gene were artificially selected during cultivated rice differentiation.

Sign in / Sign up

Export Citation Format

Share Document