Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

Download Full-text

Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽

10.1128/msystems.00448-20 ◽

2020 ◽

Vol 5 (5) ◽

Author(s):

Zhiqiu Yin ◽

Si Zhang ◽

Yi Wei ◽

Meng Wang ◽

Shuangshuang Ma ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Evolutionary Dynamics ◽

Genomic Analysis ◽

Comparative Genomic ◽

Content Type ◽

Pan Genome ◽

Long Time ◽

Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

Download Full-text

The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

Horticulture Research ◽

10.1038/s41438-020-00382-1 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Xian-Gui Yi ◽

Xia-Qing Yu ◽

Jie Chen ◽

Min Zhang ◽

Shao-Wei Liu ◽

...

Keyword(s):

Plant Disease Resistance ◽

De Novo ◽

Genomic Analysis ◽

Gene Families ◽

Single Copy ◽

Comparative Genomic ◽

Sequencing Technologies ◽

History Of ◽

Flowering Cherry ◽

Plant Disease Resistance Genes

Abstract Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

Download Full-text

Missing Millions: The Demographic Costs of the Mexican Revolution

Mexican Studies/Estudios Mexicanos ◽

10.1525/msem.2003.19.2.367 ◽

2003 ◽

Vol 19 (2) ◽

pp. 367-400 ◽

Cited By ~ 13

Author(s):

Robert McCaa

Keyword(s):

Civil War ◽

Spanish Civil War ◽

International Conflict ◽

Mexican Revolution ◽

Demographic History ◽

The Past ◽

Human Cost ◽

History Of ◽

Age And Sex ◽

The Revolution

The Mexican Revolution was a demographic disaster, but there is little agreement about the human cost or its demographic components. Were the missing millions due to war deaths, epidemics, emigration, lost births, or simply census error or evasion? Reading the demographic history of the Revolution from a subsequent census, such as the highly regarded enumeration of 1930, yields more precise figures than those obtained from the usual benchmark, the census of 1921. The 1930 figures are of better quality and, therefore, more suitable for making an assessment by age and sex. This analysis shows that in terms of lives lost, the Mexican Revolution was a demographic catastrophe, comparable to the Spanish Civil War, which has been ranked the ninth deadliest international conflict over the past two centuries. La Revolucióón Mexicana fue un desastre demográáfico; sin embargo, no existe consenso en el monto de la péérdida demográáfica ni de sus componentes. ¿¿Los millones perdidos fueron por la emigracióón, la mortalidad por epidemias, las muertes por la guerra, la caíída en el núúmero de nacimientos, o simplemente error estadíístico? Leyendo la historia demográáfica de la Revolucióón de un censo posterior, como por ejemplo el de 1930, ya que goza de reconocimiento por su calidad y confiabilidad, puede llevarse a cifras, por sexo y edad, mejor fundamentadas. En téérminos de las péérdidas de vidas, las nuevas estimaciones colocan a la Revolucióón Mexicana, junto con la Guerra Civil Españñola, como la novena guerra con mayor mortalidad en el contexto internacional, en los úúltimos dos siglos.

Download Full-text

RecPD: A Recombination-Aware Measure of Phylogenetic Diversity

10.1101/2021.10.01.462747 ◽

2021 ◽

Author(s):

Cedoljub Bundalovic-Torma ◽

Darrell Desveaux ◽

David S Guttman

Keyword(s):

Pseudomonas Syringae ◽

Evolutionary History ◽

Phylogenetic Diversity ◽

Evolutionary Dynamics ◽

Gene Families ◽

Ancestral State ◽

History Of ◽

Preliminary Study ◽

Potential Impact ◽

Study Type

A critical step in studying biological features (e.g., genetic variants, gene families, metabolic capabilities, or taxa) underlying traits or outcomes of interest is assessing their diversity and distribution. Accurate assessments of these patterns are essential for linking features to traits or outcomes and understanding their functional impact. Consequently, it is of crucial importance that the metrics employed for quantifying feature diversity can perform robustly under any evolutionary scenario. However, the standard metrics used for quantifying and comparing the distribution of features, such as prevalence, phylogenetic diversity, and related approaches, either do not take into consideration evolutionary history, or assume strictly vertical patterns of inheritance. Consequently, these approaches cannot accurately assess diversity for features that have undergone recombination or horizontal transfer. To address this issue, we have devised RecPD, a novel recombination-aware phylogenetic-diversity metric for measuring the distribution and diversity of features under all evolutionary scenarios. RecPD utilizes ancestral-state reconstruction to map the presence / absence of features onto ancestral nodes in a species tree, and then identifies potential recombination events in the evolutionary history of the feature. We also derive a number of related metrics from RecPD that can be used to assess and quantify evolutionary dynamics and correlation of feature evolutionary histories. We used simulation studies to show that RecPD reliably identifies evolutionary histories under diverse recombination and loss scenarios. We then apply RecPD in a real-world scenario in a preliminary study type III effector protein families secreted by the plant pathogenic bacterium Pseudomonas syringae and demonstrate that prevalence is an inadequate metric that obscures the potential impact of recombination. We believe RecPD will have broad utility for revealing and quantifying complex evolutionary processes for features at any biological level.

Download Full-text

Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation

10.1101/2020.07.13.200204 ◽

2020 ◽

Author(s):

Ke Cao ◽

Zhen Peng ◽

Xing Zhao ◽

Yong Li ◽

Kuozhan Liu ◽

...

Keyword(s):

High Altitude ◽

Molecular Mechanisms ◽

De Novo ◽

Genomic Analysis ◽

Gene Families ◽

Wild Relatives ◽

Comparative Genomic ◽

High Altitude Adaptation ◽

Pan Genome ◽

Altitude Adaptation

AbstractAs a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

Download Full-text

POPULATION CHANGES IN OTTOMAN ANATOLIA DURING THE 16TH AND 17TH CENTURIES: THE “DEMOGRAPHIC CRISIS” RECONSIDERED

International Journal of Middle East Studies ◽

10.1017/s0020743804362021 ◽

2004 ◽

Vol 36 (2) ◽

pp. 183-205 ◽

Cited By ~ 17

Author(s):

Oktay Özel

Keyword(s):

Ottoman Empire ◽

Quantitative Data ◽

Demographic History ◽

17Th Century ◽

Population Pressure ◽

16Th Century ◽

Central Theme ◽

Population Changes ◽

The Past ◽

History Of

The historiography of the past two decades of the demographic history of 16th- and 17th-century Ottoman Anatolia has seen diverse and often conflicting arguments among historians. Whether the Ottoman Empire witnessed “population pressure” in the 16th century, and whether this was followed in the 17th century by a serious “demographic crisis,” considered by some historians as a “catastrophe,” have constituted the central theme of the debate. The roots of these issues can be traced as far back as the early works of Ömer Lütfi Barkan in the 1940s and 1950s. It appears that the disagreements not only arose as a result of the different models of historical demography developed by diverse schools of thought, but that they also owed much to the highly disputed nature of the sources that provide the bulk of quantitative data for the demographic history of the Ottoman Empire.

Download Full-text

From Calabar to Carter's Grove: The History of a Virginia Slave Community. By Lorena S. Walsh. Charlottesville and London: University Press of Virginia, 2001. Pp. xxii, 335. $18.95, paper.

The Journal of Economic History ◽

10.1017/s0022050701005770 ◽

2001 ◽

Vol 61 (4) ◽

pp. 1140-1141

Author(s):

Peter A. Coclanis

Keyword(s):

African American ◽

Social History ◽

American History ◽

Demographic History ◽

African American History ◽

Agricultural History ◽

Quarter Century ◽

The Past ◽

The Social ◽

History Of

Over the past quarter century, no scholar has done more to document the social history of the colonial Chesapeake than Lorena Walsh. In so doing, she has made important scholarly contributions in a variety of areas, most notably, in agricultural history, demographic history, African American history, and women's history. Along with such scholars as Lois Green Carr, Allan Kulikoff, Darrett and Anita Rutman, and Russell Menard among others in the so-called Chesapeake School, Walsh has helped to create a powerful framework for understanding the evolution of Virginia and Maryland and for interpreting the behavior of the populations residing therein. Two of the hallmarks of the work of scholars associated with the “School” are innovative methodologies and meticulous, painstaking research, both of which characteristics are readily apparent in the volume under review.

Download Full-text

The natural adaptation and human selection history of African sheep genomes

10.1101/2021.11.17.469022 ◽

2021 ◽

Author(s):

Abulgasim M Ahbara ◽

Christelle Robert ◽

Adebabay Kebede ◽

Ayele Abebe ◽

Suliman Latairish ◽

...

Keyword(s):

Genomic Analysis ◽

Gene Families ◽

Comparative Genomic ◽

Selection History ◽

Ear Morphology ◽

Geographic Origins ◽

History Of ◽

Pleiotropic Gene ◽

Fat Depot ◽

Human Selection

African sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of ∼54x for 130 samples (Ethiopia, Libya) and ∼10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.

Download Full-text

Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis

Frontiers in Plant Science ◽

10.3389/fpls.2021.643548 ◽

2021 ◽

Vol 12 ◽

Author(s):

Radka Vozárová ◽

Veit Herklotz ◽

Aleš Kovařík ◽

Yuri O. Tynkevich ◽

Roman A. Volkov ◽

...

Keyword(s):

Diploid Species ◽

5S Rdna ◽

Woody Species ◽

Nucleolar Organizer ◽

Gene Families ◽

Nucleolar Organizer Regions ◽

Intergenic Spacers ◽

History Of ◽

35S Rdna ◽

Distinct Distribution

The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.

Download Full-text

iHam and pyHam: visualizing and processing hierarchical orthologous groups

Bioinformatics ◽

10.1093/bioinformatics/bty994 ◽

2018 ◽

Vol 35 (14) ◽

pp. 2504-2506 ◽

Cited By ~ 8

Author(s):

Clément-Marie Train ◽

Miguel Pignatelli ◽

Adrian Altenhoff ◽

Christophe Dessimoz

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Gene Families ◽

Comparative Genomic ◽

Last Common Ancestor ◽

Analysis Method ◽

Ancestral Gene ◽

Genomic Analyses ◽

History Of ◽

Multiple Species

Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.

Download Full-text