Draft genome of the Reindeer (Rangifer tarandus)

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

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A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology

PeerJ ◽

10.7717/peerj.9114 ◽

2020 ◽

Vol 8 ◽

pp. e9114 ◽

Cited By ~ 1

Author(s):

Jiawei Wang ◽

Weizhen Liu ◽

Dongzi Zhu ◽

Xiang Zhou ◽

Po Hong ◽

...

Keyword(s):

Sweet Cherry ◽

Prunus Avium ◽

Reference Genome ◽

De Novo ◽

Draft Genome ◽

Single Copy ◽

Sequencing Data ◽

Sequencing Technology ◽

High Quality ◽

Eukaryotic Genes

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

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Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis

GigaScience ◽

10.1093/gigascience/giz128 ◽

2019 ◽

Vol 8 (11) ◽

Cited By ~ 4

Author(s):

Sihan Lu ◽

Jie Yang ◽

Xuelei Dai ◽

Feiang Xie ◽

Jinwu He ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Demographic History ◽

Repetitive Sequences ◽

Population Expansion ◽

Chromatin Interaction ◽

Interglacial Period ◽

Last Interglacial ◽

High Quality ◽

Chromosome Level

AbstractBackgroundPapilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies.FindingsWe obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69–36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period.ConclusionsWe present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C–based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.

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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽

10.3390/ani11082226 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2226

Author(s):

Sazia Kunvar ◽

Sylwia Czarnomska ◽

Cino Pertoldi ◽

Małgorzata Tokarska

Keyword(s):

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Model Organism ◽

Genotyping By Sequencing ◽

Model Organisms ◽

European Bison ◽

Model Animal ◽

Pcr Duplicates ◽

Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

10.1101/2021.11.23.469778 ◽

2021 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Nitrogen Fixation ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Genome Wide ◽

A Genome ◽

Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing

10.1101/2021.01.08.426014 ◽

2021 ◽

Author(s):

Chi yang ◽

Lu Ma ◽

Donglai Xiao ◽

Xiaoyu Liu ◽

Xiaoling Jiang ◽

...

Keyword(s):

Repetitive Sequences ◽

Draft Genome ◽

Edible Mushroom ◽

Illumina Hiseq ◽

Protein Coding ◽

Long Reads ◽

Oxford Nanopore ◽

Genome Features ◽

Long Read ◽

Genomic Studies

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low quality genome of S. latifolia was obtained by Illumina HiSeq 2500 sequencing. These limitations in the available genome have constrained genetic and genomic studies in this mushroom resource. Herein, an updated draft genome sequence of S. latifolia was generated by Oxford Nanopore sequencing and the Hi-C technique. A total of 8.24 Gb of Oxford Nanopore long reads representing ~198.08X coverage of the S. latifolia genome were generated. Subsequently, a high-quality genome of 41.41 Mb, with scaffold and contig N50 sizes of 3.31 Mb and 1.51 Mb, respectively, was assembled. Hi-C scaffolding of the genome resulted in 12 pseudochromosomes containing 93.56% of the bases in the assembled genome. Genome annotation further revealed that 17.47% of the genome was composed of repetitive sequences. In addition, 13,103 protein-coding genes were predicted, among which 98.72% were functionally annotated. BUSCO assay results further revealed that there were 92.07% complete BUSCOs. The improved chromosome-scale assembly and genome features described here will aid further molecular elucidation of various traits, breeding of S. latifolia, and evolutionary studies with related taxa.

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De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Genes ◽

10.3390/genes10060426 ◽

2019 ◽

Vol 10 (6) ◽

pp. 426 ◽

Cited By ~ 3

Author(s):

Daniel Berner ◽

Marius Roesti ◽

Steven Bilobram ◽

Simon K. Chan ◽

Heather Kirk ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Gene Annotation ◽

Model System ◽

Threespine Stickleback ◽

Evolutionary Genomics ◽

Digital Repository ◽

High Quality ◽

De Novo Gene ◽

Dna Libraries

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7).

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Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines

Scientific Data ◽

10.1038/s41597-020-00684-y ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Mikhail Rayko ◽

Aleksey Komissarov ◽

Jason C. Kwan ◽

Grace Lim-Fong ◽

Adelaide C. Rhodes ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Transcriptome Data ◽

Biomedical Sciences ◽

Bugula Neritina ◽

Genome Sequences ◽

Illumina Hiseq ◽

Draft Assembly ◽

Metazoan Genome ◽

Animal Phyla

Abstract Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

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De novo assembly of the cattle reference genome with single-molecule sequencing

GigaScience ◽

10.1093/gigascience/giaa021 ◽

2020 ◽

Vol 9 (3) ◽

Cited By ~ 35

Author(s):

Benjamin D Rosen ◽

Derek M Bickhart ◽

Robert D Schnabel ◽

Sergey Koren ◽

Christine G Elsik ◽

...

Keyword(s):

Single Molecule ◽

De Novo Assembly ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Future Research ◽

Protein Coding ◽

Single Molecule Sequencing ◽

Assembly Accuracy ◽

Genomic Tools

Abstract Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

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Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads

10.1101/345983 ◽

2018 ◽

Cited By ~ 2

Author(s):

Huilong Du ◽

Chengzhi Liang

Keyword(s):

Single Molecule ◽

High Efficiency ◽

Reference Genome ◽

Repetitive Sequences ◽

Sequencing Data ◽

High Quality ◽

Single Molecule Sequencing ◽

Genome Maps ◽

Long Reads ◽

Novel Method

AbstractDue to the large number of repetitive sequences in complex eukaryotic genomes, fragmented and incompletely assembled genomes lose value as reference sequences, often due to short contigs that cannot be anchored or mispositioned onto chromosomes. Here we report a novel method Highly Efficient Repeat Assembly (HERA), which includes a new concept called a connection graph as well as algorithms for constructing the graph. HERA resolves repeats at high efficiency with single-molecule sequencing data, and enables the assembly of chromosome-scale contigs by further integrating genome maps and Hi-C data. We tested HERA with the genomes of rice R498, maize B73, human HX1 and Tartary buckwheat Pinku1. HERA can correctly assemble most of the tandemly repetitive sequences in rice using single-molecule sequencing data only. Using the same maize and human sequencing data published by Jiao et al. (2017) and Shi et al. (2016), respectively, we dramatically improved on the sequence contiguity compared with the published assemblies, increasing the contig N50 from 1.3 Mb to 61.2 Mb in maize B73 assembly and from 8.3 Mb to 54.4 Mb in human HX1 assembly with HERA. We provided a high-quality maize reference genome with 96.9% of the gaps filled (only 76 gaps left) and several incorrectly positioned sequences fixed compared with the B73 RefGen_v4 assembly. Comparisons between the HERA assembly of HX1 and the human GRCh38 reference genome showed that many gaps in GRCh38 could be filled, and that GRCh38 contained some potential errors that could be fixed. We assembled the Pinku1 genome into 12 scaffolds with a contig N50 size of 27.85 Mb. HERA serves as a new genome assembly/phasing method to generate high quality sequences for complex genomes and as a curation tool to improve the contiguity and completeness of existing reference genomes, including the correction of assembly errors in repetitive regions.

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The first high-quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa

10.22541/au.162012034.41527060/v1 ◽

2021 ◽

Author(s):

Liang Xu ◽

Shengnan Li ◽

Yanyun Yang ◽

Yanping Xing ◽

Zhongren Zhang ◽

...

Keyword(s):

Candidate Genes ◽

Developmental Stages ◽

Repetitive Sequences ◽

Draft Genome ◽

Edible Plant ◽

High Quality ◽

Protein Coding ◽

Arctium Lappa ◽

Coa Ligase ◽

Highly Correlated

Arctium lappa has a long medicinal and edible history with great economic importance. We combined Illumina and PacBio sequences to generate the first high-quality chromosome-level draft genome of A. lappa. The assembled genome is approximately 1.79 Gb with a N50 contig size of 6.88 Mb. Approximately 1.70 Gb (95.4%) of the contig sequences were anchored onto 18 chromosomes using Hi-C data; the scaffold N50 was improved to be 91.64 Mb. Furthermore, we obtained 1.12 Gb (68.46%) of repetitive sequences and 32,771 protein-coding genes; 616 positively selected candidate genes were identified. Additionally, we compared the transcriptomes of A. lappa roots at three different developmental stages and identified 8,943 differentially expressed genes (DEGs) in these tissues. Among candidate genes related to lignan biosynthesis, the following were found to be highly correlated with the accumulation of arctiin: 4-coumarate-CoA ligase (4CL), dirigent protein (DIR), and hydroxycinnamoyl transferase (HCT). These data can be utilized to identify genes related to A. lappa quality or provide a basis for molecular identification and comparative genomics among related species.

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