scholarly journals Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

2021 ◽  
Author(s):  
Xingtan Zhang ◽  
Shuai Chen ◽  
Longqing Shi ◽  
Daping Gong ◽  
Shengcheng Zhang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Evolutionary History ◽  
Green Revolution ◽  
Genomic Analysis ◽  
Tea Plant ◽  
Specific Expression ◽  
History Of ◽  
Allele Specific ◽  
Tea Cultivar

AbstractTea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.

scholarly journals Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Min Zhang ◽  
Delong Meng ◽  
Xueduan Liu ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

scholarly journals The unexpected survival of an ancient lineage of anseriform birds into the Neogene of Australia: the youngest record of Presbyornithidae

2016 ◽  
Vol 3 (2) ◽  
pp. 150635 ◽  
Author(s):  
Vanesa L. De Pietri ◽  
R. Paul Scofield ◽  
Nikita Zelenkov ◽  
Walter E. Boles ◽  
Trevor H. Worthy
Keyword(s):  
Evolutionary History ◽  
South Australia ◽  
First Record ◽  
South American ◽  
Crown Group ◽  
Term Survival ◽  
Skeletal Morphology ◽  
Ancient Lineage ◽  
History Of

Presbyornithids were the dominant birds in Palaeogene lacustrine assemblages, especially in the Northern Hemisphere, but are thought to have disappeared worldwide by the mid-Eocene. Now classified within Anseriformes (screamers, ducks, swans and geese), their relationships have long been obscured by their strange wader-like skeletal morphology. Reassessment of the late Oligocene South Australian material attributed to Wilaru tedfordi , long considered to be of a stone-curlew (Burhinidae, Charadriiformes), reveals that this taxon represents the first record of a presbyornithid in Australia. We also describe the larger Wilaru prideauxi sp. nov. from the early Miocene of South Australia, showing that presbyornithids survived in Australia at least until ca 22 Ma. Unlike on other continents, where presbyornithids were replaced by aquatic crown-group anatids (ducks, swans and geese), species of Wilaru lived alongside these waterfowl in Australia. The morphology of the tarsometatarsus of these species indicates that, contrary to other presbyornithids, they were predominantly terrestrial birds, which probably contributed to their long-term survival in Australia. The morphological similarity between species of Wilaru and the Eocene South American presbyornithid Telmabates antiquus supports our hypothesis of a Gondwanan radiation during the evolutionary history of the Presbyornithidae. Teviornis gobiensis from the Late Cretaceous of Mongolia is here also reassessed and confirmed as a presbyornithid. These findings underscore the temporal continuance of Australia’s vertebrates and provide a new context in which the phylogeny and evolutionary history of presbyornithids can be examined.

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

scholarly journals Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora

2015 ◽  
Author(s):  
Kim A. Steige ◽  
Benjamin Laenen ◽  
Johan Reimegård ◽  
Douglas Scofield ◽  
Tanja Slotte
Keyword(s):  
Evolutionary Biology ◽  
Genomic Analysis ◽  
Purifying Selection ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Specific Expression ◽  
Regulatory Variation ◽  
Wide Range ◽  
Allele Specific ◽  
Selective Forces

Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation are 1) under weaker purifying selection and 2) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene-body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby TEs and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide novel evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage-sensitivity of body-methylated genes. Given the extensive conservation of gene-body methylation in flowering plants, this suggests that gene-body methylation could be an important predictor of cis-regulatory variation in a wide range of plant species.

scholarly journals Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhizhu Zhao ◽  
Dongna Ma
Keyword(s):  
Camellia Sinensis ◽  
Function Analysis ◽  
Gc Content ◽  
Tea Plant ◽  
Pentose Phosphate ◽  
Specific Expression ◽  
Phenotypic Alteration ◽  
Genome Wide ◽  
The Rich ◽  
Lineage Specific Genes

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

scholarly journals Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dayana E. Salas-Leiva ◽  
Eelco C. Tromer ◽  
Bruce A. Curtis ◽  
Jon Jerlström-Hultqvist ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Origin Recognition Complex ◽  
Common Ancestor ◽  
Genomic Analysis ◽  
Free Living ◽  
A Genome ◽  
History Of ◽  
Eukaryotic Dna ◽  
Comparative Genomics Analysis ◽  
Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

scholarly journals Deep time diversity and the early radiations of birds

2021 ◽  
Vol 118 (10) ◽  
pp. e2019865118
Author(s):  
Yilun Yu ◽  
Chi Zhang ◽  
Xing Xu
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Evolutionary Rate ◽  
Rapid Evolution ◽  
Morphological Data ◽  
Deep Time ◽  
The Third ◽  
Time Diversity ◽  
History Of

Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous–Paleogene (K–Pg) extinction.

scholarly journals Power, competition, and the nature of history

Paleobiology ◽  
2019 ◽  
Vol 45 (4) ◽  
pp. 517-530 ◽  
Author(s):  
Geerat J. Vermeij
Keyword(s):  
High Frequency ◽  
Evolutionary History ◽  
Metabolic Evolution ◽  
Competition And Cooperation ◽  
The Past ◽  
Directional Change ◽  
History Of ◽  
Repeated Evolution ◽  
Ecosystem Level

AbstractHistorians have debated whether pathways and events from the past to the present are influenced largely by contingency, the dependence of outcomes on particular prior conditions, or whether there is long-term emergent directional change. Previous arguments for predictability in evolutionary history relied on the high frequency of convergence, but the repeated evolution of widely favored adaptations need not imply long-term directionality. Using evidence from the fossil record and arguments concerning the metabolic evolution of organisms, I show here that power (total energy taken up and expended per unit time) has increased stepwise over time at ecosystem-level and global scales thanks to the ratchet-like, cumulative effects of competition and cooperation and to the disproportionate influence of powerful top competitors and opportunistic species on emergent ecosystem properties and processes. The history of life therefore exhibits emergent directionality at large ecosystem-wide scales toward greater power.

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