scholarly journals First draft Genome of Loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the Evolution of Cavefish

2021 ◽  
Author(s):  
Zhi-Jin Liu ◽  
Xiong-Fei Zhang ◽  
Hua-Mei Wen ◽  
Ling Han ◽  
Jiang Zhou
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Draft Genome ◽  
Evolutionary Process ◽  
Integrated Approach ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Cave Environment ◽  
Surface Dwelling ◽  
Paired End Sequencing

Abstract BackgroundLoaches from the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth, and some species of loach inhabit the underground drainage. The genus Oreonectes with 18 currently recognized loach species represent the three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable research resource of the evolution of cavefishes.ResultWe assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. The genome assembly contains 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. Meanwhile,we found that dozens of genes related to eye development and melanogenesis were pseudogenised during the evolutionary process in cave environment, providing novel insights into complex phenotypic adaptations of animals in specific environment. ConclusionHere we report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. This genome assembly will contribute to the study of the evolution and adaptation of cavefishes within Oreonectes and beyond (Cobitidea) and provid valuable genomic resources for studies on the evolutionary history of the rapid speciation processes of family Nemacheilidae.

scholarly journals First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

2021 ◽  
Author(s):  
Zhijin Liu ◽  
Xuekun Qian ◽  
Ziming Wang ◽  
Huamei Wen ◽  
Ling Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Eye Development ◽  
Draft Genome ◽  
Evolutionary Process ◽  
Integrated Approach ◽  
Sequencing Data ◽  
Retina Development ◽  
Draft Genome Assembly ◽  
Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

scholarly journals A New High-Quality Draft Genome Assembly of the Chinese Cordyceps Ophiocordyceps sinensis

2020 ◽  
Vol 12 (7) ◽  
pp. 1074-1079 ◽  
Author(s):  
Ruihao Shu ◽  
Jihong Zhang ◽  
Qian Meng ◽  
Huan Zhang ◽  
Guiling Zhou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Tibet Plateau ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Ophiocordyceps Sinensis ◽  
Homologous Protein ◽  
Genome Features

Abstract Ophiocordyceps sinensis (Berk.) is an entomopathogenic fungus endemic to the Qinghai-Tibet Plateau. It parasitizes and mummifies the underground ghost moth larvae, then produces a fruiting body. The fungus-insect complex, called Chinese cordyceps or “DongChongXiaCao,” is not only a valuable traditional Chinese medicine, but also a major source of income for numerous Himalayan residents. Here, taking advantage of rapid advances in single-molecule sequencing, we assembled a highly contiguous genome assembly of O. sinensis. The assembly of 23 contigs was ∼110.8 Mb with a N50 length of 18.2 Mb. We used RNA-seq and homologous protein sequences to identify 8,916 protein-coding genes in the IOZ07 assembly. Moreover, 63 secondary metabolite gene clusters were identified in the improved assembly. The improved assembly and genome features described in this study will further inform the evolutionary study and resource utilization of Chinese cordyceps.

scholarly journals Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a fragmented IHHNV EVE sequence

2021 ◽  
Author(s):  
Roger Huerlimann ◽  
Jeff A Cowley ◽  
Nicholas M Wade ◽  
Yinan Wang ◽  
Naga Kasinadhuni ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Penaeus Monodon ◽  
Penaeid Shrimp ◽  
Protein Coding ◽  
Black Tiger Shrimp ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Tiger Shrimp ◽  
Endogenous Viral Elements

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements (EVEs) have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such EVEs and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of EVEs. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for one generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific EVEs identified an element comprised of a 9,045 bp stretch of repeated, inverted and jumbled genome fragments of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) bounded by a repeated 591/590 bp host sequence. As only near complete linear ~4 kb IHHNV genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear EVE types. The existence of conjoined inverted IHHNV genome fragments also provides a means by which hairpin dsRNAs could be expressed and processed by the shrimp RNA interference (RNAi) machinery.

scholarly journals A draft genome assembly of the eastern banjo frog Limnodynastes dumerilii dumerilii (Anura: Limnodynastidae)

2020 ◽  
Author(s):  
Qiye Li ◽  
Qunfei Guo ◽  
Yang Zhou ◽  
Huishuang Tan ◽  
Terry Bertozzi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Draft Genome ◽  
Protein Coding ◽  
Large Genome ◽  
Draft Genome Assembly ◽  
Protein Coding Genes ◽  
Repeat Content ◽  
Australian Continent ◽  
Large Genome Size ◽  
Reference Genomes

AbstractAmphibian genomes are usually challenging to assemble due to large genome size and high repeat content. The Limnodynastidae is a family of frogs native to Australia, Tasmania and New Guinea. As an anuran lineage that successfully diversified on the Australian continent, it represents an important lineage in the amphibian tree of life but lacks reference genomes. Here we sequenced and annotated the genome of the eastern banjo frog Limnodynastes dumerilii dumerilii to fill this gap. The total length of the genome assembly is 2.38 Gb with a scaffold N50 of 285.9 kb. We identified 1.21 Gb of non-redundant sequences as repetitive elements and annotated 24,548 protein-coding genes in the assembly. BUSCO assessment indicated that more than 94% of the expected vertebrate genes were present in the genome assembly and the gene set. We anticipate that this annotated genome assembly will advance the future study of anuran phylogeny and amphibian genome evolution.

scholarly journals A chromosome-level draft genome of the grain aphid Sitobion miscanthi

GigaScience ◽  
2019 ◽  
Vol 8 (8) ◽  
Author(s):  
Xin Jiang ◽  
Qian Zhang ◽  
Yaoguo Qin ◽  
Hang Yin ◽  
Siyu Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Acyrthosiphon Pisum ◽  
Draft Genome ◽  
Chromosome Length ◽  
Trophic Levels ◽  
Final Size ◽  
Entire Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Environmentally Safe

AbstractBackgroundSitobion miscanthi is an ideal model for studying host plant specificity, parthenogenesis-based phenotypic plasticity, and interactions between insects and other species of various trophic levels, such as viruses, bacteria, plants, and natural enemies. However, the genome information for this species has not yet to be sequenced and published. Here, we analyzed the entire genome of a parthenogenetic female aphid colony using Pacific Biosciences long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly.ResultsThe final draft genome assembly from 33.88 Gb of raw data was ∼397.90 Mb in size, with a 2.05 Mb contig N50. Nine chromosomes were further assembled based on Hi-C data to a 377.19 Mb final size with a 36.26 Mb scaffold N50. The identified repeat sequences accounted for 26.41% of the genome, and 16,006 protein-coding genes were annotated. According to the phylogenetic analysis, S. miscanthi is closely related to Acyrthosiphon pisum, with S. miscanthi diverging from their common ancestor ∼25.0–44.9 million years ago.ConclusionsWe generated a high-quality draft of the S. miscanthi genome. This genome assembly should help promote research on the lifestyle and feeding specificity of aphids and their interactions with each other and species at other trophic levels. It can serve as a resource for accelerating genome-assisted improvements in insecticide-resistant management and environmentally safe aphid management.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals The chromosome-level draft genome of Dalbergia odorifera

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Zhou Hong ◽  
Jiang Li ◽  
Xiaojin Liu ◽  
Jinmin Lian ◽  
Ningnan Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Populus Trichocarpa ◽  
Draft Genome ◽  
Heartwood Formation ◽  
Genetic Studies ◽  
Protein Coding ◽  
Dalbergia Odorifera ◽  
Paired End Sequencing ◽  
Chromosome Level

Abstract Background Dalbergia odorifera T. Chen (Fabaceae) is an International Union for Conservation of Nature red-listed tree. This tree is of high medicinal and commercial value owing to its officinal, insect-proof, durable heartwood. However, there is a lack of genome reference, which has hindered development of studies on the heartwood formation. Findings We presented the first chromosome-scale genome assembly of D. odorifera obtained on the basis of Illumina paired-end sequencing, Pacific Biosciences single-molecule real-time sequencing, 10x Genomics linked reads, and Hi-C technology. We assembled 97.68% of the 653.45 Mb D. odorifera genome with scaffold N50 and contig sizes of 56.16 and 5.92 Mb, respectively. Ten super-scaffolds corresponding to the 10 chromosomes were assembled, with the longest scaffold reaching 79.61 Mb. Repetitive elements account for 54.17% of the genome, and 30,310 protein-coding genes were predicted from the genome, of which ∼92.6% were functionally annotated. The phylogenetic tree showed that D. odorifera diverged from the ancestor of Arabidopsis thaliana and Populus trichocarpa and then separated from Glycine max and Cajanus cajan. Conclusions We sequence and reveal the first chromosome-level de novo genome of D. odorifera. These studies provide valuable genomic resources for the research of heartwood formation in D. odorifera and other timber trees. The high-quality assembled genome can also be used as reference for comparative genomics analysis and future population genetic studies of D. odorifera.

scholarly journals Chromosomal-level genome assembly of the bioluminescent cardinalfish Siphamia tubifer, an emerging model for symbiosis research

2021 ◽  
Author(s):  
Alison L Gould ◽  
James B Henderson ◽  
Athena W Lam
Keyword(s):  
Genome Assembly ◽  
Muscle Development ◽  
Draft Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Microbial Symbiosis ◽  
Symbiosis Research ◽  
Siphamia Tubifer

The bioluminescent symbiosis between the sea urchin cardinalfish Siphamia tubifer (Kurtiformes: Apogonidae) and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate-bacteria model for the study of microbial symbiosis. However, there is little genetic data available for the host fish, limiting the scope of potential research that can be carried out with this association. In this study, we present a chromosomal-level genome assembly of S. tubifer using a combination of PacBio HiFi sequencing and Hi-C technologies. The final genome assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO completeness score of 99%. A comparison of the S. tubifer genome to that of another non-luminous cardinalfish revealed a high degree of synteny, whereas a similar comparison to a more distant relative in the Gobiiformes order revealed a fusion of two chromosomes in the cardinalfish genomes. An additional comparison of orthologous clusters among these three genomes revealed a set of 710 clusters that were unique to S. tubifer in which 23 GO pathways were significantly enriched, including several relating to host-microbe interactions and one involved in visceral muscle development, which could be related to the musculature involved in the gut-associated light organ of S. tubifer. We also assembled the complete mitogenome of S. tubifer and discovered both an inversion in the WANCY tRNA gene region resulting in a WACNY gene order as well as heteroplasmy in the length of the control region for this individual. A phylogenetic analysis based on the whole mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, bringing up questions of the involvement of the bioluminescent symbiosis in the initial divergence of the ancestral Siphamia species. This draft genome assembly of S. tubifer will enable future studies investigating the evolution of bioluminescence in fishes as well as candidate genes involved in the symbiosis and will provide novel opportunities to use this system as a vertebrate-bacteria model for symbiosis research.

scholarly journals ONT-based draft genome assembly and annotation of Alternaria atra

2021 ◽  
Author(s):  
Bhawna Bonthala ◽  
Corinn Sophia Small ◽  
Maximilian Anton Lutz ◽  
Alexander Graf ◽  
Stefan Krebs ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Plant Pathogens ◽  
Biocontrol Agent ◽  
Reference Genome ◽  
Gene Prediction ◽  
Draft Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Reference Genome Assembly ◽  
Wide Range

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

scholarly journals The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

2021 ◽  
Author(s):  
Thomas W Woehner ◽  
Ofere Francis Emeriewen ◽  
Alexander Wittenberg ◽  
Harrie Schneiders ◽  
Ilse Vrijenhoek ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Sour Cherry ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Long Read ◽  
Chromosome Level

Background: Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding: The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ~6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to ~190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. Conclusion: This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

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