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

2019 ◽  
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.

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

GigaScience ◽  
2020 ◽  
Vol 9 (3) ◽  
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.

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

2018 ◽  
Author(s):  
Meng Wu ◽  
Jamie L. Kostyun ◽  
Leonie C. Moyle
Keyword(s):  
Gene Prediction ◽  
Phylogenetic Analyses ◽  
Large Fraction ◽  
Gene Families ◽  
Single Copy ◽  
Reproductive Trait ◽  
Gene Trees ◽  
Protein Coding ◽  
Solanaceae Species ◽  
High Level

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.

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

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.

scholarly journals Structural and Comparative Analysis of the Complete Chloroplast Genome of Pyrus hopeiensis—“Wild Plants with a Tiny Population”—and Three Other Pyrus Species

2018 ◽  
Vol 19 (10) ◽  
pp. 3262 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Longfei Li ◽  
Lijuan Gao ◽  
Jintao Xu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Population Decline ◽  
Gc Content ◽  
Single Copy ◽  
Wild Plants ◽  
Similar Degree ◽  
Protein Coding ◽  
Chloroplast Genomes ◽  
Close Relationship ◽  
History Of

Pyrus hopeiensis is a valuable wild resource of Pyrus in the Rosaceae. Due to its limited distribution and population decline, it has been listed as one of the “wild plants with a tiny population” in China. To date, few studies have been conducted on P. hopeiensis. This paper offers a systematic review of P. hopeiensis, providing a basis for the conservation and restoration of P. hopeiensis resources. In this study, the chloroplast genomes of two different genotypes of P. hopeiensis, P. ussuriensis Maxin. cv. Jingbaili, P. communis L. cv. Early Red Comice, and P. betulifolia were sequenced, compared and analyzed. The two P. hopeiensis genotypes showed a typical tetrad chloroplast genome, including a pair of inverted repeats encoding the same but opposite direction sequences, a large single copy (LSC) region, and a small single copy (SSC) region. The length of the chloroplast genome of P. hopeiensis HB-1 was 159,935 bp, 46 bp longer than that of the chloroplast genome of P. hopeiensis HB-2. The lengths of the SSC and IR regions of the two Pyrus genotypes were identical, with the only difference present in the LSC region. The GC content was only 0.02% higher in P. hopeiensis HB-1. The structure and size of the chloroplast genome, the gene species, gene number, and GC content of P. hopeiensis were similar to those of the other three Pyrus species. The IR boundary of the two genotypes of P. hopeiensis showed a similar degree of expansion. To determine the evolutionary history of P. hopeiensis within the genus Pyrus and the Rosaceae, 57 common protein-coding genes from 36 Rosaceae species were analyzed. The phylogenetic tree showed a close relationship between the genera Pyrus and Malus, and the relationship between P. hopeiensis HB-1 and P. hopeiensis HB-2 was the closest.

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

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.

scholarly journals The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)

2020 ◽  
Vol 12 (6) ◽  
pp. 860-866 ◽  
Author(s):  
Qing-Song Zhou ◽  
Arong Luo ◽  
Feng Zhang ◽  
Ze-Qing Niu ◽  
Qing-Tao Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Draft Genome ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Nesting Biology ◽  
Protein Coding ◽  
Final Assembly ◽  
Long Reads

Abstract Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.

scholarly journals Chromosomal-level reference genome of the neotropical tree Jacaranda mimosifolia D. Don

2021 ◽  
Author(s):  
Mingcheng Wang ◽  
Lei Zhang ◽  
Zhiqiang Wang
Keyword(s):  
Genome Assembly ◽  
Morphological Characteristics ◽  
Gene Families ◽  
Deciduous Tree ◽  
Protein Coding ◽  
Neotropical Tree ◽  
A Genome ◽  
Genomic Resource ◽  
Jacaranda Mimosifolia ◽  
Chromosome Level

Abstract Jacaranda mimosifolia D. Don is a deciduous tree widely cultivated in the tropics and subtropics of the world. It is famous for its beautiful blue flowers and pinnate compound leaves. In addition, this tree has great potential in environmental monitoring, soil quality improvement, and medicinal applications. However, a genome resource for J. mimosifolia has not been reported to date. In this study, we constructed a chromosome-level genome assembly of J. mimosifolia using PacBio sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼707.32 Mb in size, 688.76 Mb (97.36%) of which could be grouped into 18 pseudochromosomes, with contig and scaffold N50 values of 16.77 and 39.98 Mb, respectively. A total of 30,507 protein-coding genes were predicted, 95.17% of which could be functionally annotated. Phylogenetic analysis among 12 plant species confirmed the close genetic relationship between J. mimosifolia and Handroanthus impetiginosus. Gene family clustering revealed 481 unique, 103 significantly expanded, and 16 significantly contracted gene families in the J. mimosifolia genome. This chromosome-level genome assembly of J. mimosifolia will provide a valuable genomic resource for elucidating the genetic bases of the morphological characteristics, adaption evolution, and active compounds biosynthesis of J. mimosifolia.

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

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.

scholarly journals Chromosomal-Level Genome Assembly of Silver Sillago (Sillago Sihama)

2020 ◽  
Author(s):  
Xinghua Lin ◽  
Yang Huang ◽  
Dongneng Jiang ◽  
Huapu Chen ◽  
Siping Deng ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Marine Aquaculture ◽  
Inshore Waters ◽  
Sillago Sihama ◽  
Sequencing Platforms ◽  
Genome Scale

Abstract Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93% of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51% of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of S. sinica about 7.92 million years ago. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.

scholarly journals Bioaccumulation of Metals/Metalloids and Histological and Immunohistochemical Changes in the Tissue of the European Hake, Merluccius merluccius (Linnaeus, 1758) (Pisces: Gadiformes: Merlucciidae), for Environmental Pollution Assessment

2020 ◽  
Vol 8 (9) ◽  
pp. 712
Author(s):  
Antonio Salvaggio ◽  
Roberta Pecoraro ◽  
Chiara Copat ◽  
Margherita Ferrante ◽  
Alfina Grasso ◽  
...  
Keyword(s):  
Fish Species ◽  
Inductively Coupled Plasma ◽  
Pollution Assessment ◽  
Hepatic Tissue ◽  
Trophic Chain ◽  
Merluccius Merluccius ◽  
Commercial Fish ◽  
Coastal Species ◽  
High Level ◽  
European Hake

Pollution and other types of environmental stress do not spare marine environments, especially those affected by high industrial pressure. Fish, especially coastal species, are used for monitoring the marine environment because they are particularly efficient as bioindicators thanks to their ability to bioaccumulate and biomagnify along the trophic chain. The aim of this research is to evaluate the bioaccumulation and the indirect bioindication ability of the European Hake, Merluccius merluccius (Linnaeus, 1758), one of the most important commercial fish species of the Mediterranean Sea. Morphological and histological alterations of the main target organs, such as liver and gills, have been investigated and the results showed a steatosis in the hepatic tissue. The accumulation of heavy metals has been analyzed by inductively coupled plasma mass spectrometry and for several metals it was showed a different concentration in the two sexes. Moreover, the expression of metallothioneins 1 and Heat Shock Protein 70 has been assessed by immunohistochemistry and did not show high level of expression. We underline the importance of contamination evaluation in commercial fish species and the utilization of the ichthyofauna as bioindicator of environmental quality.

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