scholarly journals Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sabyasachi Mukherjee ◽  
Zexi Cai ◽  
Anupama Mukherjee ◽  
Imsusosang Longkumer ◽  
Moonmoon Mech ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genomic Architecture

scholarly journals Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

2020 ◽  
Author(s):  
Sabyasachi Mukherjee ◽  
Zexi Cai ◽  
Anupama Mukherjee ◽  
Imsusosang Longkumer ◽  
Moonmoon Mech ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genomic Architecture

scholarly journals Sequencing, De Novo Assembly, and Annotation of the Complete Genome of a New Thraustochytrid Species, Strain CCAP_4062/3

2018 ◽  
Vol 6 (11) ◽  
Author(s):  
Khawla Seddiki ◽  
François Godart ◽  
Riccardo Aiese Cigliano ◽  
Walter Sanseverino ◽  
Mohamed Barakat ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
De Novo Assembly ◽  
Complete Genome ◽  
De Novo ◽  
Gc Content ◽  
Marine Species ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences

ABSTRACT Thraustochytrids are ecologically and biotechnologically relevant marine species. We report here the de novo assembly and annotation of the whole-genome sequence of a new thraustochytrid strain, CCAP_4062/3. The genome size was estimated at 38.7 Mb with 11,853 predicted coding sequences, and the GC content was scored at 57%.

scholarly journals Whole-Genome Sequence of Pantoea americana Strain VS1, an Extended-Spectrum β-Lactamase-Producing Epibiont Isolated from Magnolia grandiflora

2017 ◽  
Vol 5 (46) ◽  
Author(s):  
Pushpa Lata ◽  
Subramaniam S. Govindarajan ◽  
Feng Qi ◽  
Jian-Liang Li ◽  
Santosh K. Maurya ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences ◽  
Central Florida ◽  
Magnolia Grandiflora ◽  
Extended Spectrum

ABSTRACT Pantoea americana strain VS1, an extended-spectrum β-lactamase-producing epibiont, was isolated from Magnolia grandiflora in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 191 contigs spanning 5,412,831 bp, with a GC content of 57.3% and comprising 4,836 predicted coding sequences.

scholarly journals The complete genome sequence of Stevia rebaudiana, the Sweetleaf

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 751
Author(s):  
Kathleen O'Neill ◽  
Stacy Pirro
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Related Species ◽  
Complete Genome ◽  
De Novo ◽  
Stevia Rebaudiana ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Link Type ◽  
Sequence Read Archive

The Sweetleaf (Stevia rebaudiana: Asteraceae) is widely grown for use as a sweetener.  We present the whole genome sequence and annotation of this species.  A total of 146,838,888 paired-end reads consisting of 22.2G bases were obtained by sequencing one leaf from a commercially grown seedling.  The reads were assembled by a de-novo method followed by alignment to related species.   Annotation was performed via GenMark-ES. The raw and assembled data is publicly available via GenBank: Sequence Read Archive (SRR6792730) and Assembly (GCA_009936405).

scholarly journals Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

2021 ◽  
Author(s):  
Tofazzal Islam ◽  
Nadia Afroz ◽  
ChuShin Koh ◽  
M. Nazmul Haque ◽  
Md. Jillur Rahman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
De Novo ◽  
Agricultural Research ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

scholarly journals De Novo Whole-Genome Sequence of Pantoea latae Strain AS1, Isolated from Zamia floridana Rhizosphere in Central Florida, USA

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Pushpa Lata ◽  
Subramaniam S. Govindarajan ◽  
Feng Qi ◽  
Jian-Liang Li ◽  
Santosh K. Maurya ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences ◽  
Central Florida

ABSTRACT Pantoea latae strain AS1 was isolated from the rhizophere of a cycad, Zamia floridana, in central Florida, USA. Here, we report the de novo whole-genome sequence of this strain, which consists of a total of 83 contigs spanning 4,960,415 bp, with a G+C content of 59.6%, and comprising 4,527 predicted coding sequences.

scholarly journals Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

2019 ◽  
Author(s):  
Raúl A. González-Pech ◽  
Yibi Chen ◽  
Timothy G. Stephens ◽  
Sarah Shah ◽  
Amin R. Mohamed ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Sequence Divergence ◽  
Whole Genome Sequence ◽  
Individual Species ◽  
Ecological Niches ◽  
Whole Genome ◽  
Structural Rearrangements ◽  
Extensive Sequence ◽  
Gene Functions

AbstractDinoflagellates of the family Symbiodiniaceae (Order Suessiales) are predominantly symbiotic, and many are known for their association with corals. The genetic and functional diversity among Symbiodiniaceae is well acknowledged, but the genome-wide sequence divergence among these lineages remains little known. Here, we present de novo genome assemblies of five isolates from the basal genus Symbiodinium, encompassing distinct ecological niches. Incorporating existing data from Symbiodiniaceae and other Suessiales (15 genome datasets in total), we investigated genome features that are common or unique to these Symbiodiniaceae, to genus Symbiodinium, and to the individual species S. microadriaticum and S. tridacnidorum. Our whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. We observed extensive structural rearrangements among symbiodiniacean genomes; those from two distinct Symbiodinium species share the most (853) syntenic gene blocks. Functions enriched in genes core to Symbiodiniaceae are also enriched in those core to Symbiodinium. Gene functions related to symbiosis and stress response exhibit similar relative abundance in all analysed genomes. Our results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This is the first comprehensive comparison of Symbiodiniaceae based on whole-genome sequence data, including comparisons at the intra-genus and intra-species levels.

scholarly journals The complete genome sequence of Toxicodendron radicans, Eastern Poison Ivy

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1015
Author(s):  
Toby Pirro ◽  
Stacy Pirro
Keyword(s):  
Contact Dermatitis ◽  
North America ◽  
Genome Sequence ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Eastern North America ◽  
Whole Genome ◽  
Link Type ◽  
Sequence Read Archive ◽  
Poison Ivy

Eastern Poison Ivy (Toxicodendron radicans, Anacardiaceae) is well known in Eastern North America for causing contact dermatitis, an itchy and painful rash in most people who come in contact with it.  We present the whole genome sequence and annotation of this species. A total of 96,255,779 paired-ends reads consisting of 28.9 G bases were obtained by sequencing one leaf from a wild-collected plant.  The reads were assembled by a de novo method followed by alignment to related species. Annotation was performed via GenMark-ES. The raw and assembled data is publicly available via GenBank: Sequence Read Archive (SRR10325927) and Assembly (GCA_009867345).

scholarly journals Improved whole genome sequence of Phytophthora capsici generated by long-read sequencing

2021 ◽  
Author(s):  
Jinxia Shi ◽  
Wenwu Ye ◽  
Dongfang Ma ◽  
Junliang Yin ◽  
Zhichao Zhang ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Economic Losses ◽  
Whole Genome ◽  
Vegetable Crops ◽  
Long Read

The soil-borne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.

scholarly journals Whole-Genome Sequence of Enterobacter sp. Strain MF024, Isolated from Soil in Shanghai, China

2019 ◽  
Vol 8 (37) ◽  
Author(s):  
Shaofeng Rong ◽  
Jin Wu ◽  
Qianqian Li ◽  
Shuo Zhang ◽  
Baoguo Cai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Ehrlich Pathway ◽  
Potential Use

We report here the draft genome sequence of Enterobacter sp. strain MF024, a bacterium that can biosynthesize 2-phenylethanol through both the Ehrlich pathway and a de novo pathway. It has potential use for the production of 2-phenylethanol.

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