Genome List

We perform genome decoding for each variety that shows phenotypic differences in quality such as rice taste, environmental stress, or disease resistance.


✓ Secure high-quality genome sequences for each breed that meet the genome analysis performance evaluation standards
✓ Discovery of new genes related to major breeding that could not be confirmed compared to IRGSP 1.0
✓ Identification of presence-absence variation (PAV), a breeding-related gene that contributes to genetic diversity and has a significant impact on phenotypic variation
✓ Secure specific and common genes for each variety and analyze evolution patterns of genes related to expansion and breeding
Discovery of markers for early selection of individuals according to breeding goals such as multiplicity and disease resistance

Overview

 The Tartary buckwheat (Fagopyrum tataricum) genome project was initiated through the Post genome Program by a consortium led by Yul Ho Kim, Su Jeong Kim, Hwang Bae Sohn, Sunghoon Lee, Dong-Ha Oh, Sin-Gi Park. 

 De novo genome sequencing of tartary buckwheat began in the early of 2014 and was completed lately in 2017. To obtain a high-quality draft genome assembly, we produced total 43.83 and 32.17 Gb sequences from Illumina paired-ends (PE) and Single-Molecule Real-Time (SMRT) sequencing platforms, respectively, which corresponded to 70x (Illumina PE) and 52x (SMRT) coverages. A hybrid assembly followed by scaffolding, gap-filling, and cleaning of redundancy resulted in a final draft assembly of 526.94 Mb in 2,566 scaffolds with 50% of the total sequence captured in 156 scaffolds larger than 886,968 bps (N50). We predicted total 43,771 putative protein-coding gene models occupying 19.33% of the genome, while 52.00% consisted of repetitive sequences and transposable elements, with Gypsy family long terminal repeat (LTR) retrotransposons being the most abundant class. We are currently preparing to publish a paper about the draft genome of tartary buckwheat. 

Statistics

Genome

Approximately 526.94Mb arranged in 2,566 scaffolds

Approximately 565.10Mb arranged in 4,433 contigs 

Scaffold N50 = 886,968bp

Contig N50 = 463,432bp

137 scaffolds larger than 1 Mbps, with above 50% of the genome in 156 scaffolds

Loci

Total 43,771 putative protein-coding gene models were predicted.  

Sequencing, Assembly, and Annotation

Genome sequencing

 We prepared both short read (Illumina)and long read (PacBio) libraries to cover the entire genome of entire genome of F. tataricum. Sequencing libraries were prepared from genomic DNA using Illumina HiSeq2500 (2 × 101 bp) and PacBio RSII platforms (>3Kb). In brief, a short insert (350 bp) paired-end (PE) library was constructed using TruSeq DNA library Prep Kit (Illumina) according to the manufacturer instructions. Single Molecule Real Time (SMRT) bell libraries were prepared from the large scale amplified cDNA as recommended by Pacific Biosciences (Palo Alto, U.S.A). SMRT bell templates were bound to polymerase using the DNA polymerase binding kit P6 v2 primers. 

How was the assembly generated?

 Whole genome de novo assembly for F. tataricum was performed via hybrid approach as follows: Long SMRT sequencing reads were assembled using Fast Alignment andCONsensus (FALCON) (Chin et al., 2016), whereas 350-bp short insert reads were assembledusing SOAPdenovo2 (Luo et al., 2012) with default parameters. Before assembly, all Illuminareads were subjected to preprocessing (adapter, quality, duplicates trimming). The initialcontigs were merged two assemblies using HaploMerger2 (Huang et al., 2017). Both shortand long reads were then used to construct scaffolds with SSPACE software (Boetzer et al.,2011) followed by gaps were filled with the short read data using GapFiller (Nadalin et al.,2012). We used CoGE SynMap (Lyons et al., 2008) and LASTZ (Kiełbasa et al., 2011) todetect and filter out redundant genomic regions (>98% sequence identity over >7Kb) togenerate the final draft assembly. The hybrid assembly resulted in a final draft assembly of 526.94 Mb in 2,566 scaffolds with 50% of the total sequence captured in 156 scaffolds larger than 886,968 bps (N50).

Is it accurate?

 To test the accuracy of the genome assembly, we applied classical Sanger sequencing methods on two BAC clones of 121.85Kb and 61.50Kb that contain gene loci for the homologs of two previously known Fagopyrum FLS coding sequences. The 121.85Kb BAC clone (“29-J17”) contained a gene locus for FtFLS1 (NCBI GenBank ID: JF27561), while the 61.50Kb BAC clone (“32-I01”) included a locus for a partial sequence of putative FLS (GenBank ID: HM357805). Both BAC clone sequences, assembled from contigs generated by Sanger sequencing, showed >99% sequence identity with their corresponding genomic regions in the draft genome assembly.

Gene prediction 

We predicted gene models in the draft genomes of F. tataricum cv. Daegwan by combining evidence from transcriptome and protein sequence alignments with ab initio prediction on repeat-masked genome sequences. GeneMark-ET (Lomsadze et al., 2014) was used to perform iterative training and to generate initial gene structures with RNA-Seq data information. AUGUSTUS (Stanke and Morgenstern, 2005) was further used to perform  de novo prediction with gene models trained by GeneMark-ET, with exon-intron boundary information predicted by transcriptome and protein sequence alignments. We used TopHat (Trapnell et al., 2012) for RNA-Seq alignment and Exonerate(Slater and Birney, 2005) for protein sequence alignment with similar species sequences. We annotated deduced protein sequences through BLASTP searches with an e-value cutoff of 1e-10 460 against NCBI  non-redundant database, UniProt, and Interproscan. Occurrence and frequency of repeats, including retrotransposons, DNA transposons, microsatellites, and other repeats, were screened using RepeatMasker (Tarailo-Graovac and Chen, 2009). Further, the repeat masked scaffolds were used for gene prediction as described above.

Is it complete?

 Compared to the draft genome of F. tataricum cv. Pinku, the problem was that the number of annotated genes and duplicated BUSCO was high in the draft genome of F. tataricum cv. Daegwan. And so, we are currently working on improving the draft genome of F. tataricum cv. Daegwan.

Contacts

Overview

Antheraea yamamai, also known as the Japanese oak silk moth, is a wild species of silk moth. Silk produced by A. yamamai, referred to as tensan silk, differs drastically from common silk produced from the domesticated silkworm, Bombyx mori. Silk moths can be categorized into two families- Bombycidae and Saturniidae. Saterniidae has been estimated to contain approximately 1,861 species with 162 genera and is known as the largest family in Lepidoptera. Among the many species in family Saturniidae, only a few species, including A. yamamai, can be utilized for silk production. For whole genome sequencing, we selected one male sample (Ay-7-male1) from a breeding line (Ay-7) of A. yamamai raised at the National Academy of Agricultural Science, Rural Development Administration, Korea. A total of 147Gb of genomic data and 76Gb of transcriptomic data was generated for this study. We present the genome sequence of A. yamamai, the first published genome in family Saturniidae, with gene expression data collected from ten different body organ tissues.

Statistics

Genome

A total of 147G base pairs using Illumina and Pacbio sequencing platforms were generated. Approximately 210-fold coverage based on the 700 Mb estimated genome size of A. yamamai. The assembled genome of A. yamamai was 656 Mb(>2kb) with 3,675 scaffolds.

The N50 length of assembly was 739 Kb with 34.07% GC ratio.

Identified repeat elements covered 37.33% of the total genome and the completeness of the constructed genome assembly was estimated to be 96.7% by BUSCO v2 analysis.

Loci

A total of 76Gb of transcriptomic data was generated for this study.

A total of 21,124 genes were identified using Evidence Modeler based on the gene prediction results obtained from 3 different methods (ab initio, RNA-seq based, known-gene based).

Assembly

Before conducting genome assembly, we conducted k-mer distribution analysis using a 350bp paired-end library in order to estimate the size and characteristics of the A. yamamai genome. The 19-mer distribution of A. yamamai genome using a 350 bp paired-end library.

In the 19-mer distribution analysis, the genome size of A. yamamai was estimated to be 709Mb. Next, we conducted error correction on Illumina paired-end libraries using the error correction module of Allpaths-LG before the initial contig assembly process (ALLPATHS-LG , RRID:SCR_010742). After error correction, initial contig assembly with 350bp and 700bp libraries was conducted using SOAP denovo2 with the parameter option set at K=19; this approach showed the best assembly statistics compared to other assemblers and parameters (SOAPdenovo2 , RRID:SCR_014986).

At each scaffolding step, SOAP Gapcloser[21] with -l 155 and -p 31 parameters was repeatedly used to close the gaps within each scaffold.

After scaffolding was performed using SSPACE-LongRead with Illumina synthetic long read data, the total number of assembled scaffolds was effectively reduced from 398,446 to 24,558. The average scaffold length was also extended from 1.7 Kb to 24.8 Kb. However, there was no impressive improvement in N50 length (approximately 91 Kb to 112 Kb) of assembled scaffolds.

After final scaffolding processing using Pacbio long reads, the number of scaffolds was reduced to 3,675 and N50 length was effectively extended from 112 Kb to 739 Kb.

Gene Prediction

Three different algorithms were used for gene prediction of the A. yamamai genome: ab initio, RNA-seq transcript based, and protein homology-based approaches.

For RNA-seq transcript based prediction, generated transcriptome data from ten organ tissues of A. yamamai were aligned to the assembled genome and gene information was predicted using Cufflinks[44](Cufflinks , RRID:SCR_014597). The longest CDS sequences were identified from Cufflinks results using Transdecoder. For the homology-based approach, all known genes of order Lepidoptera in the NCBI database were aligned using PASA. The final gene set of A. yamamai genome contains 21,124 genes.

The average gene length was 8,331 bp with a 38.76% GC ratio and the number of exons per gene was 4.44. To identify the function of predicted genes, Swiss-Prot, Uniref100, NCBI NR database, and gene information of B. mori and D. melanogaster was employed for sequence similarity search using blastp.

Contacts

Overview

Overview

We sequenced a reference strain of H. marmoreus (Haemi 51987–8). We evaluated various assembly strategies, and as a result the Allpaths and PBJelly produced the best assembly. The resulting genome was 42.7 Mbp in length and annotated with 16,627 gene models. A putative gene (Hypma_04324) encoding the antifungal and antiproliferative hypsin protein with 75% sequence identity with the previously known N-terminal sequence was identified. Carbohydrate active enzyme analysis displayed the typical feature of white-rot fungi where auxiliary activity and carbohydrate-binding modules were enriched. The genome annotation revealed four terpene synthase genes responsible for terpenoid biosynthesis. From the gene tree analysis, we identified that terpene synthase genes can be classified into six clades. Four terpene synthase genes of H. marmoreus belonged to four different groups that implies they may be involved in the synthesis of different structures of terpenes. A terpene synthase gene cluster was well-conserved in Agaricomycetes genomes, which contained known biosynthesis and regulatory genes.

Statistics

Genome

Approximately 42.71 Mb arranged in 235 scaffolds

Approximately 42.68 Mb arranged in 278 contigs (~0.06% gap)

Scaffold N50 (L50) = 17 (764.8 kbp)

Contig N50 (L50) = 20 (621.3 kbp)

83 scaffolds larger than 50 Kbp, with 96.68% of the genome in scaffolds larger than 50 Kbp

Assembly

We selected the Allpaths+PBJelly assembly for further analyses. The final assembly had a size of 42,710,661 bp including 235 scaffolds/278 contigs with 287.3× sequence coverage. The GC percentage was 49.64%. We estimated the genome size as 43.0 Mbp using the k-mer frequency calculation of Illumina paired-end reads.

NCBI GenBank Recoreds

Release Date: 25/7/2018              BioProject: PRJNA312409             Accession ID: LUEZ00000000

Is it complete?

Genome completeness was calculated using BUSCO v3.0 at the gene level. Only 5 of 1335 single-copy entries were missing, indicating >99% genome completeness. Its RNA-seq reads were mapped into the genome, where 97.27% of the reads were aligned.

Is it accurate?

The transcriptome assembly is aligned with the genome with >99% identity. Also, 97.35% of predicted genes are complete, implying accurate genome assembly without sequencing or assembly error.

What about polyploidy?

It's haploid genome.

Gene prediction

Using the FunGAP pipeline (Min, 2017), we predicted 16,627 protein-coding genes with an average size of 1586.1 nt. Of these protein-coding genes, 14,179 genes (85.3%) were supported by assembled transcripts, and this included

10,522 (63.3%) highly supported genes (> 90% coverage). The quality of the gene prediction was evaluated by comparing the predictions of three programs inside the FunGAP pipeline: Augustus 3.2.1 (Stanke, 2005), Braker 1.8 (Hoff, 2016), and Maker 2.31.8 (Cantarel, 2008). Approximately half of the predicted genes were functionally annotated; in total, 7786 genes (46.8%) were annotated using Pfam domains, and 7447 genes (44.8%) were annotated using SwissProt. The dominant functions included WD, F-box, protein kinase, cytochrome P450, and major facilitator superfamily domains, similarly as observed in other mushroom genomes (Gupta, 2018, Yuan, 2017). The genome contained 1793 genes encoding secreted proteins. We identified 1262 noncoding RNA elements containing 171 tRNAs, including 9 selenocysteine tRNAs, 191 small nucleolar RNAs (snoRNAs) from 127 different families, and 224 microRNAs from 90 different families.

References:

Min B, Grigoriev IV, Choi IG. FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation. Bioinformatics (Oxford, England). 2017;33(18):2936–7. 24. Stanke M, Morgenstern B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 2005; 33(Web Server):W465–7.

Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics (Oxford, England). 2016;32(5):767–9.

Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18(1):188–96.

Gupta DK, Ruhl M, Mishra B, Kleofas V, Hofrichter M, Herzog R, Pecyna MJ, Sharma R, Kellner H, Hennicke F, et al. The genome sequence of the commercially cultivated mushroom Agrocybe aegerita reveals a conserved repertoire of fruiting-related genes and a versatile suite of biopolymerdegrading enzymes. BMC Genomics. 2018;19(1):48.

Overview

The chrysanthemum genome project was conducted through the National Agricultural Genome Program (NAGP) and National Institute of Agricultural Sciences (NAS) Program, Republic of Korea.

Chrysanthemum boreale (Asteraceae;Asteroideae;Anthemideae) is a perennial plant native to Eastern Asia and has been used for ornamental and herbal purposes. C. boreale is a diploid species (2n=2x=18) and is close to the commercial and cultivated species, Chrysanthemum morifolium with a large and hexaploid genome (2n=6x=54). Therefore, C. boreale is used as a model plant in the study of cultivated chrysanthemum.

The genome was sequenced using PacBio single-molecule real-time long reads and was scaffolded into nine chromosome sequences using the Bionano optical map and the Hi-C contact map. Genome coverage is high according to the mapping rate of Illumina short reads and BUSCO analysis, although the Bionano optical map resulted in large gap during scaffolding process as shown in the total length of contigs 3.415 Gb and scaffolds 5.524 Gb. The assembled genome corresponds to the original sequences including large gap and the sequence tag (CTTAAG) generated from Bionano map. Considering this, below statistics was calculated in two ways without and with gap.

Statistics

Genome

Approximately 3.237 Gb is assembled in 9 chromosomes, with 0.181 Gb of unmapped scaffolds (w/o gap).

Approximately 4.831 Gb is assembled in 9 chromosomes, with 0.692 Gb of unmapped scaffolds (with gap).

Scaffold N50 = 379 Mb, Longest scaffold = 401 Mb (w/o gap)

Scaffold N50 = 557 Mb, Longest scaffold = 610 Mb (with gap)

Contig N50 = 218 kb, longest contig = 3.232 Mb

• Overview

The small brown planthopper (SBPH), Laodelphax striatellusFallén (Hemiptera: Delphacidae) is a hemimetabolous insect of which body size is less than 5 mm and has diploid bisexual chromosome (2n = 28 + XX or XO). SBPH is widely distributed in Asia, Europe, and Northern Africa and mainly feeds on the grass family, Poaceae. SBPH is one of the major pests against rice plant, Oryza sativaL. in East Asia. High density of SBPH could cause severe economic damage on rice plant by directly sucking and indirectly transmitting viral pathogens, rice stripe virus and rice streaked dwarf virus, with piercing mouthparts (i.e. Stylets). Rice stripe virus can be transmitted in a circulative, persistent, propagative manner by SBPH. SBPH has wing-size dimorphism (short vs. long) depending on genetic and environmental effect. A long-winged SBPH has been reported to massively migrate from China to Korea and Japan in early summer season. Nymphs of SBPH can also overwinter in temperate regions. Furthermore, SBPH has developed high resistance to diverse classes of insecticides including organophosphates, neonicotinoids, chitin biosynthesis inhibitor, etc., in the laboratory and the field. SBPH is taxonomically close to the brown planthopper (BPH), Nilaparvata luges (Stål) (Hemiptera: Delphacidae) which is another destructive rice pest, but diverse host range, different kind of virus transmission, and cold tolerance of SBPH are quite different from those of BPH. All these features could result in SBPH management problem in East Asia, so that genome-wide study through whole-genomesequencing may provide valuable insight tobetter understand the biological system of SBPH and the interrelationship among rice plant, virus,SBPH, and environmental factors and to develop new target site for pest management.

• Statistics

A draft genome of L. striatellus has been constructed by using PacBio and Illumina NGS platforms. It consists of 565Mbp in total length, 1,598 in scaffold contig number, and 806kbp in N50 size. A pseudomolecule of L. striatellus has been constructed by linkage mapping and scaffold anchoring with SNP marker after genotyping by sequencing. For publication on a draft genome and pseudomolecule of L. striatellus, more detailed analysis is in progress.

Table 1. Summary of de novo assembly for whole genome of Laodelphax striatellus with PacBio sequencing platform

• Contact information