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The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry)

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GIGASCIENCE 2018年第4期7卷 1-N.PAG页

作者： Buti, Matteo Moretto, Marco Barghini, Elena Mascagni, Flavia Natali, Lucia Brilli, Matteo Lomsadze, Alexandre Sonego, Paolo Giongo, Lara Alonge, Michael Velasco, Riccardo Varotto, Claudio Surbanovski, Nada Borodovsky, Mark Ward, Judson A. Engelen, Kristof Cavallini, Andrea Cestaro, Alessandro Sargent, Daniel James FEM Res & Innovat Ctr Dept Genom & Biol Fruit Crops Via E Mach 1 I-38010 San Michele All Adige Italy Univ Modena & Reggio Emilia Ctr Dev & Improvement Agri Food Resources BIOGEST Ple Europa 1 I-42124 Reggio Nellemilia RE Italy FEM Res & Innovat Ctr Unit Computat Biol Via E Mach 1 I-38010 San Michele All Adige Italy Univ Pisa Dept Agr Food & Environm Sci I-56124 Pisa Italy Univ Padova Agripolis Dept Agron Food Nat Resources Anim & Environm Vle Univ 16 I-35020 Legnaro PD Italy Univ Milan Dipartimento Biosci Via Celoria 26 I-20133 Milan Italy Univ Milan Ctr Ric Pediat Romeo & Enrica Invernizzi Via Celoria 26 I-20133 Milan Italy Georgia Tech Wallace H Coulter Dept Biomed Engn Atlanta GA USA Driscolls Strawberry Associates 121 Silliman Dr Watsonville CA USA FEM Res & Innovat Ctr Dept Biodivers & Mol Ecol Via E Mach 1 I-38010 San Michele All Adige Italy Driscolls Genet Ltd East Malling Enterprise Ctr New Rd East Malling ME19 6BJ Kent England

Background: The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. Findings: In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced. Conclusions: Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca. The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.

关键词： long-read sequencing evolutionary development angiosperms genome sequence transcriptomics

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Getting a head in hard soils: Convergent skull evolution and divergent allometric patterns explain shape variation in a highly diverse genus of pocket gophers (Thomomys)

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BMC evolutionary BIOLOGY 2016年第1期16卷 207页

作者： Marcy, Ariel E. Hadly, Elizabeth A. Sherratt, Emma Garland, Kathleen Weisbecker, Vera Univ Queensland Sch Biol Sci St Lucia Qld 4072 Australia Stanford Univ Dept Biol Stanford CA 94305 USA Australian Natl Univ Res Sch Biol Dept Evolut Ecol & Genet Canberra ACT 2601 Australia

Background: High morphological diversity can occur in closely related animals when selection favors morphologies that are subject to intrinsic biological constraints. A good example is subterranean rodents of the genus Thomomys, one of the most taxonomically and morphologically diverse mammalian genera. Highly procumbent, tooth-digging rodent skull shapes are often geometric consequences of increased body size. Indeed, larger-bodied Thomomys species tend to inhabit harder soils. We used geometric morphometric analyses to investigate the interplay between soil hardness (the main extrinsic selection pressure on fossorial mammals) and allometry (i.e. shape change due to size change;generally considered the main intrinsic factor) on crania and humeri in this fast-evolving mammalian clade. Results: Larger Thomomys species/subspecies tend to have more procumbent cranial shapes with some exceptions, including a small-bodied species inhabiting hard soils. Counter to earlier suggestions, cranial shape within Thomomys does not follow a genus-wide allometric pattern as even regional subpopulations differ in allometric slopes. In contrast, humeral shape varies less with body size and with soil hardness. Soft-soil taxa have larger humeral muscle attachment sites but retain an orthodont (non-procumbent) cranial morphology. In intermediate soils, two pairs of sister taxa diverge through differential modifications on either the humerus or the cranium. In the hardest soils, both humeral and cranial morphology are derived through large muscle attachment sites and a high degree of procumbency. Conclusions: Our results show that conflict between morphological function and intrinsic allometric patterning can quickly and differentially alter the rodent skeleton, especially the skull. In addition, we found a new case of convergent evolution of incisor procumbency among large-,medium-, and small-sized species inhabiting hard soils. This occurs through different combinations of allometric a

关键词： Environmental selection pressure evolutionary development Heterochrony Incisor procumbency Parallel evolution Principal component analysis Repeated evolution Subterranean niche

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Prenatal allometric trajectories and the developmental basis of postcranial phenotypic diversity in bats (Chiroptera)

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JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND developmentAL EVOLUTION 2019年第1-2期332卷 36-49页

作者： Lopez-Aguirre, Camilo Hand, Suzanne J. Koyabu, Daisuke Nguyen Truong Son Wilson, Laura A. B. Univ New South Wales Sch Biol Earth & Environm Sci PANGEA Res Ctr Sydney NSW 2052 Australia Univ Tokyo Univ Museum Dept Curatorial Studies Tokyo Japan Musashino Art Univ Dept Humanities & Sci Tokyo Japan Vietnam Acad Sci & Technol Inst Ecol & Biol Resources Dept Vertebrate Zool Hanoi Vietnam Grad Univ Sci & Technol Fac Ecol & Biol Resources Hanoi Vietnam

Most morphological and physiological adaptations associated with bat flight are concentrated in the postcranium, reflecting strong functional demands for flight performance. Despite an association between locomotory diversity and trophic differentiation, postcranial morphological diversity in bats remains largely unexplored. evolutionary developmental biology is a novel approach providing a link between the analysis of genotypic and phenotypic variation resulting from selective pressures. To quantify the morphological diversity of the postcranium in bats and to explore its developmental basis, we reconstructed the postcranial allometric trajectories of nine bat species from different prenatal developmental series, representing five families and both suborders. We tested for allometric growth in Chiroptera and also quantified levels of allometric disparity and inter-trajectory distances. Using a phylogenetic scaffold, we assessed whether ontogenetic differences reflect evolutionary relationships. We found significant allometric growth trajectories in almost all species. Interspecific trajectory distances showed lower variance within Yinpterochiroptera than within Yangochiroptera and between suborders. Each suborder occupied nonoverlapping sections of allometric space, showing changes in the growth rates of specific bones for each suborder. The allometry-corrected disparity was significantly higher in larger species. Statistically significant phylogenetic signal in our results suggests that there is an ontogenetic basis for the postcranial morphological diversity in modern bats. Ancestral state reconstruction also showed an increase in the amount of change in shape with size in the larger species studied. We hypothesize that differences in allometric patterns among bat taxa may reflect a size-dependent evolutionary constraint, whereby variability in body size and allometric patterns are associated.

关键词： allometric trajectories Chiroptera evolutionary development phenotypic diversity prenatal development

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Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms

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NEW PHYTOLOGIST 2017年第2期216卷 519-535页

作者： Ma, Qing Liu, Xiang Franks, Robert G. Xiang, Qiu-Yun (Jenny) North Carolina State Univ Dept Plant & Microbial Biol Raleigh NC 27695 USA Zhejiang Univ Coll Life Sci Minist Educ Key Lab Conservat Biol Endangered Wildlife Hangzhou 310058 Zhejiang Peoples R China

TFL1-, APT- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TEL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages.

关键词： CorAP1 Cornus CorTFL1 evolutionary development gene expression inflorescence in situ hybridization quantitative real-time polymerase chain reaction (qRT-PCR)

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Hierarchical nature of morphological integration and modularity in the human posterior face

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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2005年第1期128卷 26-34页

作者： Bastir, M Rosas, A Univ York Hull York Med Sch York YO10 5DD N Yorkshire England CSIC Museo Nacl Ciencias Nat Dept Paleobiol E-28006 Madrid Spain

Morphological integration and modularity are important points of intersection between evolution and the development of organismal form. Identification and quantification of integration are also of increasing paleoanthropological interest. In this study, the "posterior face," i.e., the mandibular ramus and its integration with the associated midline and lateral basicranium, is analyzed in lateral radiographs of 144 adult humans from three different geographic regions. The null hypothesis of homogenously pervasive morphological integration among "posterior-face" components is tested with Procrustes geometric morphometrics, partial least squares, and singular warps analysis. The results reveal statistically significant differences in integration. Only loose integrative relationships are found between midline and lateral components of the basicranium, which may indicate the presence of at least two different basicranial modules. This modularity can be interpreted in terms of spatiotemporal dissociation in the development of those basicranial structures, and gives support to hypotheses of independent phylogenetic modifications at the lateral and midline basicranium in humans. In addition, morphological integration was statistically significantly stronger between the middle cranial fossa and the mandibular ramus than between the ramus and the midline cranial base. This finding confirms previous hypotheses of a "petroso-mandibular unit," which could be a developmental consequence of well-known phylogenetic modifications in coronal topology of the posterior face and base in hominoid evolution, related to middle cranial fossa expansion. This unit could be involved in later evolutionary tendencies in the hominid craniofacial system.

关键词： craniofacial biology covariation evolutionary development partial least squares singular warps Procrustes geometric morphometrics

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Skull ontogeny in Arrhinoceratops brachyops (Ornithischia: Ceratopsidae) and other horned dinosaurs

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ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY 2015年第4期175卷 910-929页

作者： Mallon, Jordan C. Ryan, Michael J. Campbell, James A. Canadian Museum Nat Palaeobiol Ottawa ON K1P 6P4 Canada Cleveland Museum Nat Hist Dept Vertebrate Paleontol Cleveland OH 44106 USA Univ Calgary Dept Biol Sci Calgary AB T2N 1N4 Canada

Disentangling ontogenetic from interspecific variation is key to understanding biodiversity in the fossil record, yet information on growth in the ceratopsid subfamily Chasmosaurinae is sparse. Here, we describe the partial skull of a juvenile chasmosaurine, attributed to Arrhinoceratops brachyops, within the context of more mature specimens of this species, to better understand the ontogenetic transformations therein. We show that as A. brachyops matured, the postorbital horncores became longer and shifted from a posterior to an anterior inclination, the delta-shaped frill epiossifications became lower and fused to the underlying frill, and the face became more elongate. In these respects, A. brachyops closely resembled Triceratops, suggesting that these ontogenetic changes may have been common to all long-horned chasmosaurines. However, an event-paired cladistic analysis of Chasmosaurinae using a standardized matrix of 24 developmental characters reveals that the relative timing of ontogenetic events in Arrhinoceratops was more like that of Chasmosaurus, particularly in the relatively late reduction in scalloping around the frill margins. Thus, the ontogenetic similarities between Arrhinoceratops and Triceratops appear to be plesiomorphic, partly related to the retention of the elongate postorbital horncores, which are primitive for Ceratopsidae. This study elucidates the otherwise contentious evolutionary relationships of Arrhinoceratops, and highlights the importance of ontogenetic data for resolving phylogenies when morphological data from adults alone are inadequate.

关键词： event pairing evolutionary development Horseshoe Canyon Formation

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Quantitative trait loci 9 environment interactions for plant morphology vary over ontogeny in Brassica rapa

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NEW PHYTOLOGIST 2014年第2期201卷 657-669页

作者： Dechaine, Jennifer M. Brock, Marcus T. Iniguez-Luy, Federico L. Weinig, Cynthia Cent Washington Univ Dept Biol Sci Ellensburg WA 98926 USA Univ Wyoming Dept Bot Laramie WY 82071 USA Inst Invest Agr Carillanca Genet & Bioinformat Unit Agriaquaculture Nutr Genom Ctr Temuco 4780000 Chile

Growth in plants occurs via the addition of repeating modules, suggesting that the genetic architecture of similar subunits may vary between earlier- and later-developing modules. These complex environmentxontogeny interactions are not well elucidated, as studies examining quantitative trait loci (QTLs) expression over ontogeny have not included multiple environments. Here, we characterized the genetic architecture of vegetative traits and onset of reproduction over ontogeny in recombinant inbred lines of Brassica rapa in the field and glasshouse. The magnitude of genetic variation in plasticity of seedling internodes was greater than in those produced later in ontogeny. We correspondingly detected that QTLs for seedling internode length were environment-specific, whereas later in ontogeny the majority of QTLs affected internode lengths in all treatments. The relationship between internode traits and onset of reproduction varied with environment and ontogenetic stage. This relationship was observed only in the glasshouse environment and was largely attributable to one environment-specific QTL. Our results provide the first evidence of a QTLxenvironmentxontogeny interaction, and provide QTL resolution for differences between early- and later-stage plasticity for stem elongation. These results also suggest potential constraints on morphological evolution in early vs later modules as a result of associations with reproductive timing.

关键词： Brassica rapa evolutionary development modularity ontogeny phenotypic plasticity QTLxenvironment interactions quantitative trait loci (QTLs) trade-offs

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Comparative developmental genomics of sex-biased gene expression in early embryogenesis across mammals

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BIOLOGY OF SEX DIFFERENCES 2023年第1期14卷 1页

作者： Richardson, Victorya Engel, Nora Kulathinal, Rob J. J. Temple Univ Dept Biol 1900 N 12th St Philadelphia PA 19122 USA Temple Univ Fels Canc Inst Personalized Med Lewis Katz Sch Med Dept Canc Biol 3400 N Broad St Philadelphia PA 19140 USA Temple Univ Inst Genom & Evolutionary Med Philadelphia PA 19122 USA

Plain language summarySex differences are traditionally assumed to arise after the reproductive systems are set up in male and female embryos, and especially after these organs begin producing sex hormones. However, very early in embryo development, the sex chromosomes distinguish males (XY) and females (XX) and genes on these chromosomes are expressed differentially. In this study, we have analyzed gene expression data from mouse and human early embryos to determine whether there is sex-biased expression before implantation. Our results confirm that there is abundant sex-biased expression from the earliest stages of development, soon after fertilization. The comparison between human and mouse embryos shows comparable function of the sex-biased genes, although the specific genes involved differ between the two species. BackgroundMammalian gonadal sex is determined by the presence or absence of a Y chromosome and the subsequent production of sex hormones contributes to secondary sexual differentiation. However, sex chromosome-linked genes encoding dosage-sensitive transcription and epigenetic factors are expressed well before gonad formation and have the potential to establish sex-biased expression that persists beyond the appearance of gonadal hormones. Here, we apply a comparative bioinformatics analysis on a pair of published single-cell datasets from mouse and human during very early embryogenesis-from two-cell to pre-implantation stages-to characterize sex-specific signals and to assess the degree of conservation among early acting sex-specific genes and *** and regression analyses of gene expression across samples reveal that sex initially plays a significant role in overall gene expression patterns at the earliest stages of embryogenesis which potentially may be the byproduct of signals from male and female gametes during fertilization. Although these transcriptional sex effects rapidly diminish, sex-biased genes appear to form sex-speci

关键词： Sex-biased gene expression evolutionary development Genomics Mammalian embryogenesis

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A Shared Pattern of Postnatal Endocranial development in Extant Hominoids

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evolutionary BIOLOGY 2014年第4期41卷 572-594页

作者： Scott, Nadia Neubauer, Simon Hublin, Jean-Jacques Gunz, Philipp Max Planck Inst Evolutionary Anthropol Dept Human Evolut D-04103 Leipzig Germany

By comparing species-specific developmental patterns, we can approach the question of how development shapes adult morphology and contributes to the evolution of novel forms. Studies of evolutionary changes to brain development in primates can provide important clues about the emergence of human cognition, but are hindered by the lack of preserved neural tissue in the fossil record. As a proxy, we study the shape of endocasts, virtual imprints of the endocranial cavity, using 3D geometric morphometrics. We have previously demonstrated that the pattern of endocranial shape development is shared by modern humans, chimpanzees and Neanderthals after the first year of life until adulthood. However, whether this represents a common hominoid mode of development is unknown. Here, we present the first characterization and comparison of ontogenetic endocranial shape changes in a cross-sectional sample of modern humans, chimpanzees, gorillas, orangutans and gibbons. Using developmental simulations, we demonstrate that from late infancy to adulthood ontogenetic trajectories are similar among all hominoid species, but differ in the amount of shape change. Furthermore, we show that during early ontogeny gorillas undergo more pronounced shape changes along this shared trajectory than do chimpanzees, indicative of a dissociation of size and shape change. As shape differences between species are apparent in even our youngest samples, our results indicate that the ontogenetic trajectories of extant hominoids diverged at an earlier stage of ontogeny but subsequently converge following the eruption of the deciduous dentition.

关键词： Endocranium Virtual endocast evolutionary development Hominoid Heterochrony Geometric morphometrics

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Comparative ontogeny in humans and chimpanzees: Similarities, differences and paradoxes in postnatal growth and development of the skull

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ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER 2004年第5-6期186卷 503-509页

作者： Bastir, M Rosas, A CSIC Museo Nacl Ciencias Nat Dept Paleobiol E-28006 Madrid Spain

The hypothesis of retarded development is a classic and controversial issue in human evolution. It depends directly on the understanding of ontogenetic trajectories and their basic constituents: timing, rate and associated patterns of maturation. In the present study, we applied geometric morphometrics to investigate postnatal ontogeny in human and chimpanzee skulls (N = 302). We evaluated postnatal ontogenetic rates, based on comparisons of properties of size and shape in adults. At different dental ages the percentage of the adult mean size (growth) and adult mean shape (development) was used to quantify patterns of maturation. We found significantly higher levels of ontogenetic maturity in humans than chimpanzees during pre-M1 and M1 eruption. However, during this ontogenetic period the human increments were lower than those of chimpanzees suggesting lower rates. During and after M2-eruption species did not differ in their ontogenetic trajectories. The results indicate that higher prenatal and lower peri- and postnatal maturation rates characterize human ontogeny when compared with chimpanzees. If mandibular ontogeny is considered alone, a paradox was found. Whereas growth maturation proceeded in an expected trajectory continuously approximating 100% adult mean size, developmental maturity was different. After M1-eruption in both species the morphological distance, which had increased before, became reduced again, and reached adult mean shape in a second developmental peak. Such a tendency was found in humans and chimpanzees. This indicates that both size and shape maturation must be considered to understand the complexity of postnatal mandibular ontogeny.

关键词： heterochrony evolutionary development craniofacial maturation procrustes distance geometric morphometrics

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