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1.
Elife ; 102021 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-34427184

RESUMO

Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.

2.
Nat Commun ; 12(1): 4377, 2021 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-34312382

RESUMO

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.


Assuntos
Apomixia/genética , Citrus/genética , Frutas/genética , Genoma de Planta/genética , Alelos , Citrus/classificação , Extremo Oriente , Frequência do Gene , Genética Populacional , Genótipo , Geografia , Haplótipos , Hibridização Genética , Filogenia , Especificidade da Espécie
3.
Commun Biol ; 4(1): 819, 2021 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-34188187

RESUMO

Bobtail and bottletail squid are small cephalopods with striking anti-predatory defensive mechanisms, bioluminescence, and complex morphology; that inhabit nektobenthic and pelagic environments around the world's oceans. Yet, the evolution and diversification of these animals remain unclear. Here, we used shallow genome sequencing of thirty-two bobtail and bottletail squids to estimate their evolutionary relationships and divergence time. Our phylogenetic analyses show that each of Sepiadariidae, Sepiolidae, and the three subfamilies of the Sepiolidae are monophyletic. We found that the ancestor of the Sepiolinae very likely possessed a bilobed light organ with bacteriogenic luminescence. Sepiolinae forms a sister group to Rossinae and Heteroteuthinae, and split into Indo-Pacific and Atlantic-Mediterranean lineages. The origin of these lineages coincides with the end of the Tethys Sea and the separation of these regions during the Eocene and the beginning of the Oligocene. We demonstrated that sepiolids radiated after the Late Cretaceous and that major biogeographic events might have shaped their distribution and speciation.


Assuntos
Decapodiformes/genética , Evolução Molecular , Filogenia , Animais , Decapodiformes/classificação , Luminescência
5.
Annu Rev Plant Biol ; 72: 411-435, 2021 06 17.
Artigo em Inglês | MEDLINE | ID: mdl-33848428

RESUMO

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools.


Assuntos
Genoma de Planta , Genômica
6.
Plant Mol Biol ; 2021 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-33604743

RESUMO

KEY MESSAGE: We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

7.
Nat Commun ; 11(1): 5442, 2020 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-33116128

RESUMO

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.


Assuntos
Poaceae/genética , Biomassa , Cromossomos de Plantas/genética , Elementos de DNA Transponíveis , Diploide , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Variação Genética , Genoma de Planta , Genômica , Modelos Genéticos , Filogenia , Poaceae/classificação , Poaceae/crescimento & desenvolvimento , Poliploidia , Saccharum/genética , Estações do Ano , Sorghum/genética
8.
Plant J ; 104(5): 1215-1232, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32985030

RESUMO

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosome-scale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.


Assuntos
Citrus/genética , Resposta ao Choque Frio/genética , Genoma de Planta , Doenças das Plantas/genética , Poncirus/genética , Quimera , Closterovirus/patogenicidade , Resistência à Doença/genética , Evolução Molecular , Variação Genética , Anotação de Sequência Molecular , Família Multigênica , Infecções por Nematoides/genética , Doenças das Plantas/microbiologia , Doenças das Plantas/virologia , Proteínas/genética , Proteínas/metabolismo , Locos de Características Quantitativas , Seleção Genética , Fatores de Transcrição/genética
9.
Commun Biol ; 3(1): 480, 2020 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-32873878

RESUMO

Closely related muntjac deer show striking karyotype differences. Here we describe chromosome-scale genome assemblies for Chinese and Indian muntjacs, Muntiacus reevesi (2n = 46) and Muntiacus muntjak vaginalis (2n = 6/7), and analyze their evolution and architecture. The genomes show extensive collinearity with each other and with other deer and cattle. We identified numerous fusion events unique to and shared by muntjacs relative to the cervid ancestor, confirming many cytogenetic observations with genome sequence. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites. A few genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype.


Assuntos
Cromatina/genética , Evolução Molecular , Genoma , Cariótipo , Cervo Muntjac/genética , Animais , Cromossomos de Mamíferos/genética , Feminino , Filogenia
10.
Nat Ecol Evol ; 4(6): 820-830, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32313176

RESUMO

Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.


Assuntos
Evolução Molecular , Duplicação Gênica , Animais , Genoma , Sintenia , Vertebrados/genética
11.
Commun Biol ; 2: 465, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31840110

RESUMO

Bobtail squid are emerging models for host-microbe interactions, behavior, and development, yet their species diversity and distribution remain poorly characterized. Here, we combine mitochondrial and transcriptome sequences with morphological analysis to describe three species of bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu archipelago, and compare them with related taxa. One Ryukyuan type was previously unknown, and is described here as Euprymna brenneri sp. nov. Another Ryukyuan type is morphologically indistinguishable from Sepiola parva Sasaki, 1913. Molecular analyses, however, place this taxon within the genus Euprymna Steenstrup, 1887, and additional morphological investigation led to formal rediagnosis of Euprymna and reassignment of this species as Euprymna parva comb. nov. While no adults from the third Ryukyuan type were found, sequences from hatchlings suggest a close relationship with E. pardalota Reid, 2011, known from Australia and East Timor. The broadly sampled transcriptomes reported here provide a foundation for future phylogenetic and comparative studies.


Assuntos
Decapodiformes/anatomia & histologia , Decapodiformes/genética , Animais , Decapodiformes/classificação , Perfilação da Expressão Gênica , Ilhas , Tipagem Molecular , Fenótipo , Filogenia
12.
Genome Biol ; 20(1): 161, 2019 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-31399118

RESUMO

Following publication of the original article [1], the authors reported that the Availability of data and materials section required updating. The updated text reads as follows.

13.
Genome Biol ; 20(1): 126, 2019 06 21.
Artigo em Inglês | MEDLINE | ID: mdl-31227026

RESUMO

BACKGROUND: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergent subspecies. Here, we delineate the evolutionary processes driving the genetic diversity and population differentiation in this species. RESULTS: Using whole-genome re-sequencing data from 517 B. stricta accessions, we identify four genetic groups that diverged around 30-180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY), and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome, we also find regions with both high FST and dXY among the groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. CONCLUSIONS: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.


Assuntos
Brassicaceae/genética , Genoma de Planta , Polimorfismo Genético , Seleção Genética , Resistência à Doença/genética
14.
Dev Biol ; 452(1): 8-20, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30980799

RESUMO

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.


Assuntos
Mapeamento Cromossômico , Cromossomos/genética , Perfilação da Expressão Gênica , Genoma , Anotação de Sequência Molecular , Animais , Humanos , Xenopus
15.
Science ; 363(6432)2019 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-30872491

RESUMO

Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm Hofstenia miamia, a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during Hofstenia regeneration. Combining egr inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.


Assuntos
Fatores de Transcrição de Resposta de Crescimento Precoce/metabolismo , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Invertebrados/genética , Invertebrados/fisiologia , Regeneração/genética , Animais , Sítios de Ligação , Cromatina/metabolismo , Genoma , Transcriptoma , Cicatrização/genética
16.
Commun Biol ; 2: 70, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30793048

RESUMO

A persistent concern with CRISPR-Cas9 gene editing has been the potential to generate mutations at off-target genomic sites. While CRISPR-engineering mice to delete a ~360 bp intronic enhancer, here we discovered a founder line that had marked immune dysregulation caused by a 24 kb tandem duplication of the sequence adjacent to the on-target deletion. Our results suggest unintended repair of on-target genomic cuts can cause pathogenic "bystander" mutations that escape detection by routine targeted genotyping assays.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes/métodos , Subunidade alfa de Receptor de Interleucina-2/genética , Mutação , Linfócitos T Reguladores/imunologia , Linfócitos T/imunologia , Animais , Sequência de Bases , Células Cultivadas , Dano ao DNA , Reparo do DNA , Duplicação Gênica , Regulação da Expressão Gênica/imunologia , Subunidade alfa de Receptor de Interleucina-2/imunologia , Camundongos Endogâmicos NOD , Linfócitos T/metabolismo , Linfócitos T Reguladores/metabolismo
17.
Proc Natl Acad Sci U S A ; 116(8): 3030-3035, 2019 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-30635418

RESUMO

Microbes have been critical drivers of evolutionary innovation in animals. To understand the processes that influence the origin of specialized symbiotic organs, we report the sequencing and analysis of the genome of Euprymna scolopes, a model cephalopod with richly characterized host-microbe interactions. We identified large-scale genomic reorganization shared between E. scolopes and Octopus bimaculoides and posit that this reorganization has contributed to the evolution of cephalopod complexity. To reveal genomic signatures of host-symbiont interactions, we focused on two specialized organs of E. scolopes: the light organ, which harbors a monoculture of Vibrio fischeri, and the accessory nidamental gland (ANG), a reproductive organ containing a bacterial consortium. Our findings suggest that the two symbiotic organs within E. scolopes originated by different evolutionary mechanisms. Transcripts expressed in these microbe-associated tissues displayed their own unique signatures in both coding sequences and the surrounding regulatory regions. Compared with other tissues, the light organ showed an abundance of genes associated with immunity and mediating light, whereas the ANG was enriched in orphan genes known only from E. scolopes Together, these analyses provide evidence for different patterns of genomic evolution of symbiotic organs within a single host.


Assuntos
Bactérias/isolamento & purificação , Interações entre Hospedeiro e Microrganismos/genética , Octopodiformes/microbiologia , Simbiose/genética , Aliivibrio fischeri/genética , Aliivibrio fischeri/isolamento & purificação , Animais , Bactérias/classificação , Bactérias/genética , Cefalópodes/genética , Cefalópodes/microbiologia , Decapodiformes/genética , Decapodiformes/microbiologia , Genoma/genética , Octopodiformes/genética
18.
Curr Biol ; 29(2): 312-318.e3, 2019 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-30639106

RESUMO

Chaetognaths (arrow worms) are an enigmatic group of marine animals whose phylogenetic position remains elusive, in part because they display a mix of developmental and morphological characters associated with other groups [1, 2]. In particular, it remains unclear whether they are a sister group to protostomes [1, 2], one of the principal animal superclades, or whether they bear a closer relationship with some spiralian phyla [3, 4]. Addressing the phylogenetic position of chaetognaths and refining our understanding of relationships among spiralians are essential to fully comprehend character changes during bilaterian evolution [5]. To tackle these questions, we generated new transcriptomes for ten chaetognath species, compiling an extensive phylogenomic dataset that maximizes data occupancy and taxonomic representation. We employed inference methods that consider rate and compositional heterogeneity across taxa to avoid limitations of earlier analyses [6]. In this way, we greatly improved the resolution of the protostome tree of life. We find that chaetognaths cluster together with rotifers, gnathostomulids, and micrognathozoans within an expanded Gnathifera clade and that this clade is the sister group to other spiralians [7, 8]. Our analysis shows that several previously proposed groupings are likely due to systematic error, and we propose a revised organization of Lophotrochozoa with three main clades: Tetraneuralia (mollusks and entoprocts), Lophophorata (brachiopods, phoronids, and ectoprocts), and a third unnamed clade gathering annelids, nemerteans, and platyhelminthes. Consideration of classical morphological, developmental, and genomic characters in light of this topology indicates secondary loss as a fundamental trend in spiralian evolution.


Assuntos
Evolução Molecular , Invertebrados/classificação , Filogenia , Transcriptoma , Animais , Invertebrados/genética
19.
Genes (Basel) ; 9(4)2018 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-29597328

RESUMO

Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of apomictic species. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. Using a hybrid approach that combines homology-based and de novo methods 27,048 protein-coding genes were predicted. Also repeats, transfer RNA (tRNA) and ribosomal RNA (rRNA) genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. In addition, we explored the histidine exonuclease APOLLO locus, related to apomixis in Boechera, and proposed model of its evolution through the series of duplications. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species.

20.
Nature ; 554(7692): 311-316, 2018 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-29414943

RESUMO

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.


Assuntos
Citrus/classificação , Citrus/genética , Evolução Molecular , Especiação Genética , Genoma de Planta/genética , Genômica , Filogenia , Ásia Sudeste , Biodiversidade , Produção Agrícola/história , Haplótipos/genética , Heterozigoto , História Antiga , Migração Humana , Hibridização Genética
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