scholarly journals Chromosome-scale genome assembly of the high royal jelly-producing honeybees

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Lianfei Cao ◽  
Xiaomeng Zhao ◽  
Yanping Chen ◽  
Cheng Sun
Keyword(s):  
Genome Sequence ◽  
Genetic Basis ◽  
Royal Jelly ◽  
Repetitive Sequences ◽  
Chromosome Inversion ◽  
Protein Coding ◽  
Long Reads ◽  
Alignment Analysis ◽  
Shed Light ◽  
Selection Of

AbstractA high royal jelly-producing strain of honeybees (HRJHB) has been obtained by successive artificial selection of Italian honeybees (Apis mellifera ligustica) in China. The HRJHB can produce amounts of royal jelly that are dozens of times greater than their original counterparts, which has promoted China to be the largest producer of royal jelly in the world. In this study, we generated a chromosome-scale of the genome sequence for the HRJHB using PacBio long reads and Hi-C technique. The genome consists of 16 pseudo-chromosomes that contain 222 Mb of sequence, with a scaffold N50 of 13.6 Mb. BUSCO analysis yielded a completeness score of 99.3%. The genome has 12,288 predicted protein-coding genes and a rate of 8.11% of repetitive sequences. One chromosome inversion was identified between the HRJHB and the closely related Italian honeybees through whole-genome alignment analysis. The HRJHB’s genome sequence will be an important resource for understanding the genetic basis of high levels of royal jelly production, which may also shed light on the evolution of domesticated insects.

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

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.

scholarly journals Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated from Tropical Air Collected in Singapore

2018 ◽  
Vol 6 (18) ◽  
pp. e00230-18 ◽  
Author(s):  
Vineeth Kodengil Vettath ◽  
Ana Carolina M. Junqueira ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
James N. I. Houghton ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Protein Coding ◽  
Content Type ◽  
Air Samples ◽  
Protein Coding Genes ◽  
Long Reads

ABSTRACT Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

scholarly journals Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Boping Tang ◽  
Daizhen Zhang ◽  
Haorong Li ◽  
Senhao Jiang ◽  
Huabin Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Repetitive Sequences ◽  
Asia Pacific ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Protein Coding ◽  
Eukaryotic Genes ◽  
Long Reads ◽  
Commercial Species ◽  
Chromosome Level

Abstract Background The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. Findings Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. Conclusions We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.

scholarly journals Complete Genome Sequence of Curtobacterium sp. Strain SGAir0471, Isolated from Singapore Air Samples

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Phu Pwint Thin Hlaing ◽  
Ana Carolina M. Junqueira ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
Anthony Wong ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Illumina Miseq ◽  
Protein Coding ◽  
Air Samples ◽  
Protein Coding Genes ◽  
Pacbio Rs Ii ◽  
Long Reads

Curtobacterium sp. strain SGAir0471 was isolated from tropical air samples collected in Singapore. The genome was assembled using PacBio RS II long reads and Illumina MiSeq short paired-end reads. The complete genome measures 3.53 Mb and consists of 3,151 protein-coding genes, 49 tRNAs, and 12 rRNAs.

scholarly journals Draft Genome Sequence Resource for Phyllachora maydis—An Obligate Pathogen That Causes Tar Spot of Corn with Recent Economic Impacts in the United States

2020 ◽  
Vol 33 (7) ◽  
pp. 884-887
Author(s):  
Darcy E. P. Telenko ◽  
Tiffanna J. Ross ◽  
Sujoung Shim ◽  
Qinhu Wang ◽  
Raksha Singh
Keyword(s):  
United States ◽  
Genome Sequence ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
The United States ◽  
Effector Proteins ◽  
Protein Coding ◽  
Corn Breeding ◽  
Tar Spot ◽  
Obligate Pathogen

Phyllachora maydis is an important fungal pathogen that causes tar spot of corn and has led to significant yield loss in the United States and other countries. P. maydis is an obligate biotroph belonging to the Sordariomycetes class of Ascomycota. Due to the challenges posed by their obligate nature, there is no genome sequence available in the Phyllachora genus. P. maydis isolate PM01 was collected from a corn field in Indiana and the genome was determined by next-generation sequencing. The assembly size is 45.7 Mb, with 56.46% repetitive sequences. There are 5,992 protein-coding genes and 59 are predicted as effector proteins. This genome resource will increase our understanding of genomic features of P. maydis and will assist in studying the corn–P. maydis interaction and identifying potential resistant candidates for corn breeding programs.

scholarly journals Complete Genome Sequence of Brachybacterium sp. Strain SGAir0954, Isolated from Singapore Air

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
Phu Pwint Thin Hlaing ◽  
Ana Carolina M. Junqueira ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
James N. I. Houghton ◽  
...  
Keyword(s):  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Smrt Sequencing ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Reads

Brachybacterium sp. strain SGAir0954 was isolated from tropical air collected in Singapore, and its genome was sequenced and assembled using long reads generated by single-molecule real-time (SMRT) sequencing. The complete genome has a size of 3.41 Mb and consists of 2,955 protein coding genes, 50 tRNAs, and 9 rRNAs.

scholarly journals Complete Genome Sequence of Lelliottia nimipressuralis Type Strain SGAir0187, Isolated from Tropical Air Collected in Singapore

2018 ◽  
Vol 6 (18) ◽  
Author(s):  
Cassie E. Heinle ◽  
Ana Carolina M. Junqueira ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
James N. I. Houghton ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Illumina Miseq ◽  
Protein Coding ◽  
Content Type ◽  
Air Samples ◽  
Protein Coding Genes ◽  
Long Reads

ABSTRACT Lelliottia nimipressuralis type strain SGAir0187 was isolated from tropical air samples collected in Singapore. The genome was assembled with an average coverage of 180-fold using Pacific Biosciences long reads and Illumina MiSeq paired-end reads. The genome measures 4.8 Mb and contains 4,424 protein-coding genes, 83 tRNAs, and 25 rRNAs.

scholarly journals Establishment of a near-contiguous genome sequence of the citric acid producing yeast Yarrowia lipolytica DSM 3286 with resolution of rDNA clusters and telomeres

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Tobias Luttermann ◽  
Christian Rückert ◽  
Daniel Wibberg ◽  
Tobias Busche ◽  
Jan-Philipp Schwarzhans ◽  
...  
Keyword(s):  
Yarrowia Lipolytica ◽  
Genome Sequence ◽  
Fine Tuning ◽  
Rdna Cluster ◽  
Large Size ◽  
Long Reads ◽  
Genome Assemblies ◽  
Yeast Yarrowia Lipolytica ◽  
Shed Light ◽  
Specific Cluster

Abstract Yarrowia lipolytica is an oleaginous yeast that is particularly suitable for the sustainable production of secondary metabolites. The genome of this yeast is characterized by its relatively large size and its high number of different rDNA clusters located in its telomeric regions. However, due to the presence of long repetitive elements in the sub-telomeric regions, rDNA clusters and telomeres are missing in current genome assemblies of Y. lipolytica. Here, we present the near-contiguous genome sequence of the biotechnologically relevant strain DSM 3286. We employed a hybrid assembly strategy combining Illumina and nanopore sequencing reads to integrate all six rDNA clusters as well as telomeric repeats into the genome sequence. By fine-tuning of DNA isolation and library preparation protocols, we were able to create ultra-long reads that not only contained multiples of mitochondrial genomes but also shed light on the inter- and intra-chromosomal diversity of rDNA cluster types. We show that there are ten different rDNA units present in this strain that additionally appear in a predefined order in a cluster. Based on single reads, we also demonstrate that the number of rDNA repeats in a specific cluster varies from cell to cell within a population.

scholarly journals Draft Genome Sequence of Paucibacter aquatile CR182 T , a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Eu Jin Chung ◽  
Gang-Guk Choi ◽  
Young-Ho Nam ◽  
Ahyoung Choi
Keyword(s):  
Genome Sequence ◽  
Genetic Basis ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Nakdong River ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Genome Data ◽  
Adaptive Mechanisms

ABSTRACT This report details a draft genome sequence of Paucibacter aquatile CR182 T , isolated from river water, which contains 5,523,543 bp, has a G+C content of 66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data provide insights into the genetic basis of this strain’s antibacterial activity and adaptive mechanisms.

scholarly journals Draft Genome Sequence of a Bombella apis Strain Isolated from Honey Bees

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Eric A. Smith ◽  
Sylvie A. Martin-Eberhardt ◽  
Delaney L. Miller ◽  
Audrey J. Parish ◽  
Irene L. G. Newton
Keyword(s):  
Honey Bee ◽  
Genome Sequence ◽  
Honey Bees ◽  
Royal Jelly ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Larval Food ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

Bombella apis occupies a variety of distinct niches within a honey bee hive, including queen guts, royal jelly, and larval food. In an effort to better understand its evolution and identify signatures of honey bee association, we sequenced a strain isolated from hive honey stores. This genome is 2,086,308 bp long and contains 1,975 protein-coding genes.

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