Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae

ABSTRACTWithin the economically important plant family Solanaceae, Jaltomata is a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ∼80 species. Here we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long-reads (25X) and Illumina short-reads (148X) achieved an assembly of approximately 1.45 Gb, spanning ∼96% of the estimated genome. 96% of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (∼80%) of the genome, with the most recently active element, Gypsy, expanding across the genome in the last 1-2 million years.Computational gene prediction, in conjunction with a merged transcriptome dataset from 11 tissues, identified 34725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined that Jaltomata is most likely sister to Solanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression between Jaltomata and Capsicum after these species split. We also identified gene family dynamics specific to Jaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility. This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group, and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.

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Additional description and genome analyses of Caenorhabditis auriculariae representing the basal lineage of genus Caenorhabditis

Scientific Reports ◽

10.1038/s41598-021-85967-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mehmet Dayi ◽

Natsumi Kanzaki ◽

Simo Sun ◽

Tatsuya Ide ◽

Ryusei Tanaka ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Gene Families ◽

Single Copy ◽

Specific Gene ◽

Protein Coding ◽

Molecular Phylogenetic ◽

Tight Association ◽

Genome Analyses ◽

Species Specific

AbstractCaenorhabditis auriculariae, which was morphologically described in 1999, was re-isolated from a Platydema mushroom-associated beetle. Based on the re-isolated materials, some morphological characteristics were re-examined and ascribed to the species. In addition, to clarify phylogenetic relationships with other Caenorhabditis species and biological features of the nematode, the whole genome was sequenced and assembled into 109.5 Mb with 16,279 predicted protein-coding genes. Molecular phylogenetic analyses based on ribosomal RNA and 269 single-copy genes revealed the species is closely related to C. sonorae and C. monodelphis placing them at the most basal clade of the genus. C. auriculariae has morphological characteristics clearly differed from those two species and harbours a number of species-specific gene families, indicating its usefulness as a new outgroup species for Caenorhabditis evolutionary studies. A comparison of carbohydrate-active enzyme (CAZy) repertoires in genomes, which we found useful to speculate about the lifestyle of Caenorhabditis nematodes, suggested that C. auriculariae likely has a life-cycle with tight-association with insects.

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Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation

Scientific Reports ◽

10.1038/s41598-021-81784-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mingzheng Duan ◽

Haiying Bao ◽

Tolgor Bau

Keyword(s):

Life History ◽

De Novo ◽

Phylogenetic Analyses ◽

Gene Families ◽

Single Copy ◽

Mushroom Species ◽

Protein Coding ◽

Homologous Genes ◽

Metabolic Genes ◽

History Of

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.

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Chromosome-level genome assembly of the greenfin horse-faced filefish (Thamnaconus septentrionalis) using Oxford Nanopore PromethION sequencing and Hi-C technology

10.1101/798744 ◽

2019 ◽

Cited By ~ 1

Author(s):

Li Bian ◽

Fenghui Li ◽

Jianlong Ge ◽

Pengfei Wang ◽

Qing Chang ◽

...

Keyword(s):

Fish Species ◽

Population Decline ◽

Gene Families ◽

Single Copy ◽

Protein Coding ◽

Commercial Fish ◽

Marine Aquaculture ◽

West Pacific Ocean ◽

High Level ◽

Chromosome Level

AbstractThe greenfin horse-faced filefish, Thamnaconus septentrionalis, is a valuable commercial fish species that is widely distributed in the Indo-West Pacific Ocean. It has characteristic blue-green fins, rough skin and spine-like first dorsal fin. T. septentrionalis is of a conservation concern as a result of sharply population decline, and it is an important marine aquaculture fish species in China. The genomic resources of this filefish are lacking and no reference genome has been released. In this study, the first chromosome-level genome of T. septentrionalis was constructed using Nanopore sequencing and Hi-C technology. A total of 50.95 Gb polished Nanopore sequence were generated and were assembled to 474.31 Mb genome, accounting for 96.45% of the estimated genome size of this filefish. The assembled genome contained only 242 contigs, and the achieved contig N50 was 22.46 Mb, reaching a surprising high level among all the sequenced fish species. Hi-C scaffolding of the genome resulted in 20 pseudo-chromosomes containing 99.44% of the total assembled sequences. The genome contained 67.35 Mb repeat sequences, accounting for 14.2% of the assembly. A total of 22,067 protein-coding genes were predicted, of which 94.82% were successfully annotated with putative functions. Furthermore, a phylogenetic tree was constructed using 1,872 single-copy gene families and 67 unique gene families were identified in the filefish genome. This high quality assembled genome will be a valuable genomic resource for understanding the biological characteristics and for facilitating breeding of T. septentrionalis.

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Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo (Caryophyllales)

10.1101/145995 ◽

2017 ◽

Author(s):

Abigail J. Moore ◽

Jurriaan M. de Vos ◽

Lillian P. Hancock ◽

Eric Goolsby ◽

Erika J. Edwards

Keyword(s):

Molecular Evolution ◽

Phylogenetic Analyses ◽

Strong Support ◽

Gene Families ◽

Sister Group ◽

Single Copy ◽

Gene Trees ◽

Evolutionary Transitions ◽

Large Gene ◽

Cam Photosynthesis

ABSTRACTHybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, single copy loci are relatively uncommon elements of most genomes, and as such may provide a biased evolutionary history. Furthermore, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (~2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ~50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve with strong support the sister lineage of the cacti: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees for the resolution of the sister group of the cacti. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.

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A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400951 ◽

2019 ◽

Vol 10 (2) ◽

pp. 811-826 ◽

Cited By ~ 5

Author(s):

Albert Erives ◽

Bernd Fritzsch

Keyword(s):

Phylogenetic Analyses ◽

Gene Families ◽

Single Copy ◽

Gene Duplications ◽

Nervous Systems ◽

Evolutionary Diversification ◽

Transmembrane Channel ◽

Sensory Epithelia ◽

Protein X ◽

Ancient Gene

The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

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Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

Systematic Biology ◽

10.1093/sysbio/syaa063 ◽

2020 ◽

Author(s):

Matthew H Van Dam ◽

James B Henderson ◽

Lauren Esposito ◽

Michelle Trautwein

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Single Gene ◽

Gene Tree ◽

Single Copy ◽

Species Tree ◽

Bootstrap Support ◽

Gene Trees ◽

Species Trees ◽

Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

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Genomic characterization and curation of UCEs improves species tree reconstruction

10.1101/828335 ◽

2019 ◽

Author(s):

Matthew H. Van Dam ◽

James B. Henderson ◽

Lauren Esposito ◽

Michelle Trautwein

Keyword(s):

Marine Invertebrates ◽

Phylogenetic Analyses ◽

Single Gene ◽

Single Copy ◽

Species Tree ◽

Bootstrap Support ◽

Gene Trees ◽

Species Trees ◽

Tree Reconstruction ◽

Phylogenomic Analyses

ABSTRACTUltraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including; birds, mammals, fish, Hymenoptera (ants, wasps and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees were significantly improved across all datasets. Increased loci length appears to drive this increase in bootstrap support. Additionally, we found that gene trees generated from merged UCEs were more accurate than those generated by unmerged and randomly merged UCEs, based on our simulation study. This modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

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Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

Frontiers in Genetics ◽

10.3389/fgene.2021.728418 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jielong Zhou ◽

Peifu Wu ◽

Zhongping Xiong ◽

Naiyong Liu ◽

Ning Zhao ◽

...

Keyword(s):

Genome Assembly ◽

Phylogenetic Analyses ◽

Repetitive Sequences ◽

Gene Families ◽

Thaumetopoea Pityocampa ◽

High Quality ◽

Protein Coding ◽

Peptidoglycan Recognition Protein ◽

Recognition Protein ◽

Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

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A screen for gene paralogies delineating evolutionary branching order of early Metazoa

10.1101/704551 ◽

2019 ◽

Author(s):

Albert Erives ◽

Bernd Fritzsch

Keyword(s):

Phylogenetic Analyses ◽

Gene Families ◽

Single Copy ◽

Gene Duplications ◽

Nervous Systems ◽

Evolutionary Diversification ◽

Transmembrane Channel ◽

Sensory Epithelia ◽

Ancient Gene ◽

Early Metazoan

The evolutionary diversification of animals is one of Earth’s greatest triumphs, yet its origins are still shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) versus Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the MLX/MLXIP family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplication, absent in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

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Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family

GigaScience ◽

10.1093/gigascience/giaa013 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 1

Author(s):

Xupo Ding ◽

Wenli Mei ◽

Qiang Lin ◽

Hao Wang ◽

Jun Wang ◽

...

Keyword(s):

Genome Assembly ◽

Gene Annotation ◽

Draft Genome ◽

Single Copy ◽

Aquilaria Sinensis ◽

Final Size ◽

Plant Resources ◽

Protein Coding ◽

High Level ◽

Chromosome Level

Abstract Backgroud Aquilaria sinensis (Lour.) Spreng is one of the important plant resources involved in the production of agarwood in China. The agarwood resin collected from wounded Aquilaria trees has been used in Asia for aromatic or medicinal purposes from ancient times, although the mechanism underlying the formation of agarwood still remains poorly understood owing to a lack of accurate and high-quality genetic information. Findings We report the genomic architecture of A. sinensis by using an integrated strategy combining Nanopore, Illumina, and Hi-C sequencing. The final genome was ∼726.5 Mb in size, which reached a high level of continuity and a contig N50 of 1.1 Mb. We combined Hi-C data with the genome assembly to generate chromosome-level scaffolds. Eight super-scaffolds corresponding to the 8 chromosomes were assembled to a final size of 716.6 Mb, with a scaffold N50 of 88.78 Mb using 1,862 contigs. BUSCO evaluation reveals that the genome completeness reached 95.27%. The repeat sequences accounted for 59.13%, and 29,203 protein-coding genes were annotated in the genome. According to phylogenetic analysis using single-copy orthologous genes, we found that A. sinensis is closely related to Gossypium hirsutum and Theobroma cacao from the Malvales order, and A. sinensis diverged from their common ancestor ∼53.18–84.37 million years ago. Conclusions Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis. This study should contribute to valuable genetic resources for further research on the agarwood formation mechanism, genome-assisted improvement, and conservation biology of Aquilaria species.

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