scholarly journals The first draft genome of a cold-water coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae)

2020 ◽  
Author(s):  
Yang Zhou ◽  
Chenguang Feng ◽  
Yujin Pu ◽  
Jun Liu ◽  
Ruoyu Liu ◽  
...  
Keyword(s):  
Cold Water ◽  
Draft Genome ◽  
Gene Families ◽  
Single Copy ◽  
Anthropogenic Activity ◽  
Heme Binding ◽  
Protein Coding ◽  
Community Protection ◽  
Sequencing Platforms ◽  
Metabolic Regulators

Abstract Cold-water corals (CWCs) are important habitats for creatures in the deep-sea environment, but they have been degraded by anthropogenic activity. So far, no genome for any CWC has been reported. Here, we report a draft genome of Trachythela sp., which represents the first genome of CWCs to date. In total, 56 Gb and 65 Gb of raw reads were generated from Illumina and Nanopore sequencing platforms, respectively. The final assembled genome was 578.26Mb, which consisted of 396 contigs with a contig N50 of 3.56 Mb, and the genome captured 90.1% of the metazoan Benchmarking Universal Single-Copy Orthologs. We identified 335Mb (57.88% of the genome) of repetitive elements, which is a higher proportion compared with others in the Cnidarians, along with 35,305 protein-coding genes. We also detected 483 expanded and 51 contracted gene families, and many of them were associated with longevity, ion transposase, heme-binding nicotinamide adenine dinucleotide, and metabolic regulators of transcription. Overall, we believe this genome will serve as an important resource for studies on community protection for CWCs.

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 The genomes of two parasitic wasps that parasitize the diamondback moth

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Min Shi ◽  
Zhizhi Wang ◽  
Xiqian Ye ◽  
Hongqing Xie ◽  
Fei Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Diamondback Moth ◽  
Draft Genome ◽  
Gene Families ◽  
Detoxification Enzymes ◽  
Parasitic Wasps ◽  
Protein Coding ◽  
Wasp Species ◽  
Sequencing Platforms

Abstract Background Parasitic insects are well-known biological control agents for arthropod pests worldwide. They are capable of regulating their host’s physiology, development and behaviour. However, many of the molecular mechanisms involved in host-parasitoid interaction remain unknown. Results We sequenced the genomes of two parasitic wasps (Cotesia vestalis, and Diadromus collaris) that parasitize the diamondback moth Plutella xylostella using Illumina and Pacbio sequencing platforms. Genome assembly using SOAPdenovo produced a 178 Mb draft genome for C. vestalis and a 399 Mb draft genome for D. collaris. A total set that contained 11,278 and 15,328 protein-coding genes for C. vestalis and D. collaris, respectively, were predicted using evidence (homology-based and transcriptome-based) and de novo prediction methodology. Phylogenetic analysis showed that the braconid C. vestalis and the ichneumonid D. collaris diverged approximately 124 million years ago. These two wasps exhibit gene gains and losses that in some cases reflect their shared life history as parasitic wasps and in other cases are unique to particular species. Gene families with functions in development, nutrient acquisition from hosts, and metabolism have expanded in each wasp species, while genes required for biosynthesis of some amino acids and steroids have been lost, since these nutrients can be directly obtained from the host. Both wasp species encode a relative higher number of neprilysins (NEPs) thus far reported in arthropod genomes while several genes encoding immune-related proteins and detoxification enzymes were lost in both wasp genomes. Conclusions We present the annotated genome sequence of two parasitic wasps C. vestalis and D. collaris, which parasitize a common host, the diamondback moth, P. xylostella. These data will provide a fundamental source for studying the mechanism of host control and will be used in parasitoid comparative genomics to study the origin and diversification of the parasitic lifestyle.

scholarly journals Draft Genome Sequence of Bacillus sp. Strain IGA-FME-2, Isolated from the Bulk Soil of Soybean (Glycine max L.) in Northeast China

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Zhenhua Yu ◽  
Sergio de los Santos-Villalobos ◽  
Yansheng Li ◽  
Jian Jin ◽  
Fannie Isela Parra Cota ◽  
...  
Keyword(s):  
Glycine Max ◽  
Draft Genome ◽  
Gc Content ◽  
Single Copy ◽  
Bulk Soil ◽  
23S Rrna ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Glycine Max L

ABSTRACT Here, we present the draft genome of Bacillus sp. strain IGA-FME-2. This strain was isolated from the bulk soil of soybean (Glycine max L.). Its genome consists of 3,810 protein-coding genes, 44 tRNAs, two 16S rRNAs, and a single copy of 23S rRNA, with a GC content of 46.4%.

scholarly journals Draft Genome Sequence of Bacillus sp. Strain SPB7, Isolated from the Marine Sponge Spongia officinalis

2020 ◽  
Vol 9 (30) ◽  
Author(s):  
Dhruba Bhattacharya ◽  
Sergio de los Santos Villalobos ◽  
Valeria Valenzuela Ruiz ◽  
Joseph Selvin ◽  
Joydeep Mukherjee
Keyword(s):  
Genome Sequence ◽  
Marine Sponge ◽  
Draft Genome ◽  
Single Copy ◽  
5S Rrna ◽  
Bacillus Sp ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Spongia Officinalis

ABSTRACT The draft genome of Bacillus sp. SPB7, which was isolated from the marine sponge Spongia officinalis, is presented. This bacterium is a producer of an antimicrobial cyclic diketopiperazine, (3S,6S)-3,6-diisobutylpiperazine-2,5-dione. The genome consists of 4,511 protein-coding genes, 63 tRNAs, 2 16S rRNAs, 3 23S rRNAs, and a single copy of 5S rRNA.

scholarly journals Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

2020 ◽  
Author(s):  
Chao Yang ◽  
Xuejuan Li ◽  
Qingxiong Wang ◽  
Hao Yuan ◽  
Yuan Huang ◽  
...  
Keyword(s):  
Habitat Loss ◽  
Divergence Time ◽  
Single Copy ◽  
Iucn Red List ◽  
Repeat Sequence ◽  
Protein Coding ◽  
Breeding Populations ◽  
Philomachus Pugnax ◽  
Genomic Resource ◽  
Sequencing Platforms

Abstract BackgroundThe relict gull (Larus relictus), one of the least known Aves, was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation.ResultsIn this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, the first reference genome of the genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 protein-coding genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. The phylogenetic tree was constructed using 7,339 single-copy orthologous genes, which showed Charadriiformes located at the basal position and Philomachus pugnax as the closest relative of L. relictus. The divergence time between L. relictus and P. pugnax was ~68.44 Mya. The population dynamics of the Ordos breeding subpopulation in Hongjian Nur is a good confirmation that these birds are suffering from habitat loss and fragmentation.ConclusionsThis assembled genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and helps to establish a foundation for further studies investigating whether the other three breeding subpopulations have combined with the Ordos breeding subpopulation. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to improve the fragmentation of breeding populations.

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 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 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 Draft Genome Sequence of Pseudomonas stutzeri Strain KMS 55, an Endophytic Diazotroph Isolated from Rice Roots

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Kannepalli Annapurna ◽  
Venkadasamy Govindasamy ◽  
Meenakshi Sharma ◽  
Yuvika Rajrana ◽  
Karivaradharajan Swarnalakshmi ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Pseudomonas Stutzeri ◽  
Single Copy ◽  
23S Rrna ◽  
Protein Coding ◽  
Content Type ◽  
A Genome

ABSTRACT Pseudomonas stutzeri strain KMS 55 (MTCC 12703) is an isolate from the root tissues of rice (Oryza sativa L.) that displays a high biological nitrogen fixation ability. Here, we report the complete genome sequence of this strain, which contains 4,637,820 bp, 4,289 protein-coding genes, 5,006 promoter sequences, 62 tRNAs, a single copy of 5S-16S-23S rRNA, and a genome average GC content of 51.18%. Analysis of the ~4.64-Mb genome sequence will give support to increased understanding of the genetic determinants of host range, endophytic colonization behavior, endophytic nitrogen fixation, and other plant-beneficial roles of Pseudomonas stutzeri.

scholarly journals The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in Europe

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 708 ◽  
Author(s):  
Julien Alban Nguinkal ◽  
Ronald Marco Brunner ◽  
Marieke Verleih ◽  
Alexander Rebl ◽  
Lidia de los Ríos-Pérez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Gene Prediction ◽  
Draft Genome ◽  
Single Copy ◽  
Sander Lucioperca ◽  
Illumina Platform ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
And Performance

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.

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