Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus

Abstract Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

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First de novo whole genome sequencing and assembly of the bar-headed goose

PeerJ ◽

10.7717/peerj.8914 ◽

2020 ◽

Vol 8 ◽

pp. e8914 ◽

Cited By ~ 1

Author(s):

Wen Wang ◽

Fang Wang ◽

Rongkai Hao ◽

Aizhen Wang ◽

Kirill Sharshov ◽

...

Keyword(s):

High Altitude ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Gene Prediction ◽

Repetitive Sequences ◽

Gene Families ◽

Whole Genome ◽

Sequencing Data

Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.

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Amynthas corticis genome reveals molecular mechanisms behind global distribution

Communications Biology ◽

10.1038/s42003-021-01659-4 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xing Wang ◽

Yi Zhang ◽

Yufeng Zhang ◽

Mingming Kang ◽

Yuanbo Li ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Mechanisms ◽

Gene Families ◽

The Body ◽

Gene Family Evolution ◽

Complex Environments ◽

Protein Coding ◽

Itraq Analysis ◽

Rdna Sequencing ◽

Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

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ASPic-GeneID: A Lightweight Pipeline for Gene Prediction and Alternative Isoforms Detection

BioMed Research International ◽

10.1155/2013/502827 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Tyler Alioto ◽

Ernesto Picardi ◽

Roderic Guigó ◽

Graziano Pesole

Keyword(s):

Ab Initio ◽

Gene Annotation ◽

Gene Prediction ◽

Gene Prediction Program ◽

C Elegans ◽

Prediction Program ◽

First Pass ◽

Main Components ◽

Genome Projects ◽

Alternative Isoforms

New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; however, full-fledged annotation systems are usually home-grown and customized to a particular genome. There is thus a renewed need for accurateab initiogene prediction methods. However, it is apparent that fullyab initiomethods fall short of the required level of sensitivity and specificity for a quality annotation. Evidence in the form of expressed sequences gives the single biggest improvement in accuracy when used to inform gene predictions. Here, we present a lightweight pipeline for first-pass gene prediction on newly sequenced genomes. The two main components are ASPic, a program that derives highly accurate, albeit not necessarily complete, EST-based transcript annotations from EST alignments, and GeneID, a standard gene prediction program, which we have modified to take as evidence intron annotations. The introns output by ASPic CDS predictions is given to GeneID to constrain the exon-chaining process and produce predictions consistent with the underlying EST alignments. The pipeline was successfully tested on the entireC. elegansgenome and the 44 ENCODE human pilot regions.

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The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

Wellcome Open Research ◽

10.12688/wellcomeopenres.17204.1 ◽

2021 ◽

Vol 6 ◽

pp. 258

Author(s):

Konrad Lohse ◽

Alexander Mackintosh ◽

Roger Vila ◽

◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Sex Chromosome ◽

Gene Annotation ◽

Protein Coding ◽

Individual Male ◽

Protein Coding Genes ◽

A Genome ◽

Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

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TrancriptomeReconstructoR, A Data-Driven Annotation of Complex Transcriptomes

10.21203/rs.3.rs-131404/v1 ◽

2020 ◽

Author(s):

Maxim Ivanov ◽

Albin Sandelin ◽

Sebastian Marquardt

Keyword(s):

De Novo ◽

Gene Annotation ◽

R Package ◽

Sequence Information ◽

Rna Seq ◽

Sequencing Data ◽

Gene Model ◽

Preparation Methods ◽

Downstream Analysis

Abstract Background: The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for de novo transcriptome annotation. Ideally, gene and transcript models should be called from a limited set of key experimental data. Results: We developed TranscriptomeReconstructoR, an R package which implements a pipeline for automated transcriptome annotation. It relies on integrating features from independent and complementary datasets: i) full-length RNA-seq for detection of splicing patterns and ii) high-throughput 5' and 3' tag sequencing data for accurate definition of gene borders. The pipeline can also take a nascent RNA-seq dataset to supplement the called gene model with transient transcripts.We reconstructed de novo the transcriptional landscape of wild type Arabidopsis thaliana seedlings as a proof-of-principle. A comparison to the existing transcriptome annotations revealed that our gene model is more accurate and comprehensive than the two most commonly used community gene models, TAIR10 and Araport11. In particular, we identify thousands of transient transcripts missing from the existing annotations. Our new annotation promises to improve the quality of A.thaliana genome research.Conclusions: Our proof-of-concept data suggest a cost-efficient strategy for rapid and accurate annotation of complex eukaryotic transcriptomes. We combine the choice of library preparation methods and sequencing platforms with the dedicated computational pipeline implemented in the TranscriptomeReconstructoR package. The pipeline only requires prior knowledge on the reference genomic DNA sequence, but not the transcriptome. The package seamlessly integrates with Bioconductor packages for downstream analysis.

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Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽

10.3390/genes12091359 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1359

Author(s):

Esther Camacho ◽

Sandra González-de la Fuente ◽

Jose C. Solana ◽

Alberto Rastrojo ◽

Fernando Carrasco-Ramiro ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Leishmania Major ◽

De Novo ◽

Gene Annotation ◽

Leishmania Species ◽

De Novo Genome Assembly ◽

Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

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Quality of prokaryote genome assembly: Indispensable issues of factors affecting prokaryote genome assembly quality

Gene ◽

10.1016/j.gene.2012.06.016 ◽

2012 ◽

Vol 505 (2) ◽

pp. 365-367 ◽

Cited By ~ 8

Author(s):

Adriana R. Carneiro ◽

Rommel Thiago Jucá Ramos ◽

Hivana Patricia Melo Barbosa ◽

Maria Paula C. Schneider ◽

Debmalya Barh ◽

...

Keyword(s):

Genome Assembly ◽

Assembly Quality ◽

Factors Affecting

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Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

Genome Biology and Evolution ◽

10.1093/gbe/evaa016 ◽

2020 ◽

Vol 12 (2) ◽

pp. 3917-3925

Author(s):

Greer A Dolby ◽

Matheo Morales ◽

Timothy H Webster ◽

Dale F DeNardo ◽

Melissa A Wilson ◽

...

Keyword(s):

Genome Assembly ◽

Mojave Desert ◽

De Novo ◽

Stop Codon ◽

Draft Genome ◽

Gene Families ◽

Sea Turtle ◽

Desert Tortoise ◽

Draft Genome Assembly ◽

Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

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The gene-rich genome of the scallop Pecten maximus

GigaScience ◽

10.1093/gigascience/giaa037 ◽

2020 ◽

Vol 9 (5) ◽

Cited By ~ 4

Author(s):

Nathan J Kenny ◽

Shane A McCarthy ◽

Olga Dudchenko ◽

Katherine James ◽

Emma Betteridge ◽

...

Keyword(s):

Genome Assembly ◽

Gene Annotation ◽

Atlantic Coast ◽

Shallow Waters ◽

Pharmaceutical Companies ◽

Marine Bivalve ◽

Pecten Maximus ◽

Assembly Sequence ◽

Algal Toxins ◽

Large Numbers

Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. Findings Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. Conclusions The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.

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GPRED-GC: a Gene PREDiction model accounting for 5 ′- 3′ GC gradient

BMC Bioinformatics ◽

10.1186/s12859-019-3047-3 ◽

2019 ◽

Vol 20 (S15) ◽

Cited By ~ 1

Author(s):

Prapaporn Techa-Angkoon ◽

Kevin L. Childs ◽

Yanni Sun

Keyword(s):

Ab Initio ◽

Gene Annotation ◽

Gene Prediction ◽

Source Code ◽

Gc Content ◽

Prediction Tools ◽

Homologous Sequences ◽

Manual Intervention ◽

Grass Genomes ◽

Gc Contents

Abstract Background Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tools and they have been widely used for gene annotation for various species. However, existing tools are not optimized for identifying genes with highly variable GC content. In addition, some genes in grass genomes exhibit a sharp 5 ′- 3′ decreasing GC content gradient, which is not carefully modeled by available gene prediction tools. Thus, there is still room to improve the sensitivity and accuracy for predicting genes with GC gradients. Results In this work, we designed and implemented a new hidden Markov model (HMM)-based ab initio gene prediction tool, which is optimized for finding genes with highly variable GC contents, such as the genes with negative GC gradients in grass genomes. We tested the tool on three datasets from Arabidopsis thaliana and Oryza sativa. The results showed that our tool can identify genes missed by existing tools due to the highly variable GC contents. Conclusions GPRED-GC can effectively predict genes with highly variable GC contents without manual intervention. It provides a useful complementary tool to existing ones such as Augustus for more sensitive gene discovery. The source code is freely available at https://sourceforge.net/projects/gpred-gc/.

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