scholarly journals Chromosome scale reference genome of Cluster bean (Cyamopsis tetragonoloba (L.) Taub.)

2020 ◽  
Author(s):  
Kishor Gaikwad ◽  
G. Ramakrishna ◽  
Harsha Srivastava ◽  
Swati Saxena ◽  
Tanvi Kaila ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Guar Gum ◽  
Western India ◽  
Cyamopsis Tetragonoloba ◽  
Protein Coding ◽  
Cluster Bean ◽  
Gas Drilling ◽  
Oxford Nanopore ◽  
A Genome

AbstractClusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as Guar is a widely cultivated dryland legume of Western India and parts of Africa. Apart from being a vegetable crop, it is also an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan which is widely used in cosmetics, pharmaceuticals, food processing, shale gas drilling etc. Here, for the first time we are reporting a chromosome-scale reference genome assembly of clusterbean, from a high galactomannan containing popular guar cultivar, RGC-936, by combining sequenced reads from Illumina, 10x Chromium and Oxford Nanopore technologies. The initial assembly of 1580 scaffolds with an N50 value of 7.12 Mbp was generated. Then, the final genome assembly was obtained by anchoring these scaffolds to a high density SNP map. Finally, a genome assembly of 550.31 Mbp was obtained in 7 pseudomolecules corresponding to 7 chromosomes with a very high N50 of 78.27 Mbp. We finally predicted 34,680 protein-coding genes in the guar genome. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted breeding of superior cultivars.

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

scholarly journals Genome sequence resource of Phomopsis longicolla strain YC2-1, a fungal pathogen causing Phomopsis stem blight in soybean

2021 ◽  
Author(s):  
Xiaolin Zhao ◽  
Zhichao Zhang ◽  
Sujiao Zheng ◽  
Wenwu Ye ◽  
Xiaobo Zheng ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Stem Canker ◽  
Quality Data ◽  
Phomopsis Longicolla ◽  
Protein Coding ◽  
Stem Blight ◽  
A Genome ◽  
Long Read ◽  
Genomic Resource ◽  
Blight Disease

Diaporthe-Phomopsis disease complex causes considerable yield losses in soybean production worldwide. As one of the major pathogens, Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is not only the primary agent of Phomopsis seed decay, but also one of the agents of Phomopsis pod and stem blight, and Phomopsis stem canker. We performed both PacBio long read sequencing and Illumina short read sequencing, and obtained a genome assembly for the P. longicolla strain YC2-1, which was isolated from soybean stem with Phomopsis stem blight disease. The 63.1 Mb genome assembly contains 87 scaffolds, with a minimum, maximum, and N50 scaffold length of 20 kb, 4.6 Mb, and 1.5 Mb respectively, and a total of 17,407 protein-coding genes. The high-quality data expand the genomic resource of P. longicolla species and will provide a solid foundation for a better understanding of their genetic diversity and pathogenic mechanisms.

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

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.

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

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.

scholarly journals A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Reference Genome ◽  
Close Relative ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

Galactomannan content and key enzymes of its metabolism in seedsof cluster bean [Cyamopsis tetragonoloba (L.) Taub.]

2016 ◽  
Author(s):  
Neha Wadhwa ◽  
Udai Narayan Joshi
Keyword(s):  
Guar Gum ◽  
Specific Activity ◽  
Genetic Manipulation ◽  
Sharp Decrease ◽  
Cyamopsis Tetragonoloba ◽  
Key Enzymes ◽  
Cluster Bean ◽  
Activity Of Enzymes ◽  
The Mean ◽  
Mature Seeds

The present investigation was carried out to estimate galactomannan content in mature seeds of 17 guar genotypes and activity of enzymes involved in galactomannan metabolism. Galactomannan content was found in the range of 16.82 (in IC 310630) to 36.68 per cent (in HG 3-2). The developing pods were sampled at 25, 32, 39 and 46 days after flowering (DAF) for a-galactosyltransferase, ß-D-mannosidase & ß-1, 4-mannanase assay. The mean a-galactosyltransferase specific activity increased from 25 to 39 DAF (1557 to 3093 units) followed by decrease at 46 DAF (1484 units). The mean specific activity increased from 392 to 3166 units with the increase in galactomannan content from 16.82 to 36.68 per cent. Thus, this enzyme showed highly positive correlation with the galactomannan content. The mean specific activity of ß-D-mannosidase increased gradually from 25 to 39 DAF (67 to 138 units) followed by sharp decrease at 46 DAF (32 units). The mean specific activity of ß-1, 4-mannanase was found maximum at 25 DAF (102 units) and afterwards, it decreased continuously with advancement of days after flowering up to 46 days (9 units). On the whole, it can be said that the ß-D-mannosidase requires prior activity of ß-1, 4-mannanase for galactomannan catabolism while a-galactosyltransferase activity is positively correlated with galactomannan content and play a major role in guar gum synthesis and can be further used for gum improvement via genetic manipulation.

scholarly journals The genome sequence of the Glanville fritillary, Melitaea cinxia (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 266
Author(s):  
Roger Vila ◽  
Alex Hayward ◽  
Konrad Lohse ◽  
Charlotte Wright ◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Melitaea Cinxia ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual male Melitaea cinxia (the Glanville fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 499 megabases in span. The complete assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 13,666 protein coding genes.

scholarly journals Development of SNP Set for the Marker-Assisted Selection of Guar (Cyamopsis tetragonoloba (L.) Taub.) Based on a Custom Reference Genome Assembly

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2063
Author(s):  
Elizaveta Grigoreva ◽  
Yury Barbitoff ◽  
Anton Changalidi ◽  
Dmitry Karzhaev ◽  
Vladimir Volkov ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Marker Assisted Selection ◽  
Genome Wide Association Study ◽  
Reference Genome ◽  
Guar Gum ◽  
Inositol Phosphates ◽  
Inositol Phosphate ◽  
Industrial Applications ◽  
Gas Production ◽  
Cyamopsis Tetragonoloba

Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.

scholarly journals The genome sequence of the heath fritillary, Melitaea athalia (Rottemburg, 1775)

2021 ◽  
Vol 6 ◽  
pp. 304
Author(s):  
Alex Hayward ◽  
Roger Vila ◽  
Dominik R. Laetsch ◽  
Konrad Lohse ◽  
Tobias Baril ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Female ◽  
Protein Coding Genes ◽  
A Genome

We present a genome assembly from an individual female Melitaea athalia (also known as Mellicta athalia; the heath fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 610 megabases in span. In total, 99.98% of the assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 12,824 protein coding genes.

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