scholarly journals OrchidBase 4.0: a database for orchid genomics and molecular biology

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu-Yun Hsiao ◽  
Chih-Hsiung Fu ◽  
Sau-Yee Ho ◽  
Chung-I Li ◽  
You-Yi Chen ◽  
...  
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Gene Annotation ◽  
Whole Genome ◽  
Biotic And Abiotic Stress ◽  
Genome Sequences ◽  
Orchid Species ◽  
Kegg Pathways ◽  
Expressed Sequence

Abstract Background The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. Description Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. Conclusions OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/

scholarly journals Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

2020 ◽  
Author(s):  
Naoki Osada ◽  
Kazunari Matsudaira ◽  
Yuzuru Hamada ◽  
Suchinda Malaivijitnond
Keyword(s):  
Genomic Diversity ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
Whole Genome ◽  
Genome Sequences ◽  
X Chromosomes ◽  
Specific Hybridization ◽  
Predominantly Female ◽  
Chromosomal Loci

AbstractThe role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the mechanisms forming the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked genetic loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.

scholarly journals Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization

GigaScience ◽  
2018 ◽  
Vol 7 (4) ◽  
Author(s):  
Zhangyuan Pan ◽  
Shengdi Li ◽  
Qiuyue Liu ◽  
Zhen Wang ◽  
Zhengkui Zhou ◽  
...  
Keyword(s):  
Whole Genome ◽  
Genome Sequences

scholarly journals Testing sex-biased admixture origin of macaque species using autosomal and X-chromosomal genomic sequences

2020 ◽  
Author(s):  
Naoki Osada ◽  
Kazunari Matsudaira ◽  
Yuzuru Hamada ◽  
Suchinda Malaivijitnond
Keyword(s):  
Genomic Diversity ◽  
Hybrid Origin ◽  
Mitochondrial Genomes ◽  
Whole Genome ◽  
Genome Sequences ◽  
X Chromosomes ◽  
Specific Hybridization ◽  
Predominantly Female ◽  
Chromosomal Loci

Abstract The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the origins of the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.

scholarly journals Whole-Genome De Novo Sequencing of the Lignin-Degrading Wood Rot Fungus Phanerochaete chrysosporium (ATCC 20696)

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Chang-Young Hong ◽  
Su-Yeon Lee ◽  
Sun-Hwa Ryu ◽  
Sung-Suk Lee ◽  
Myungkil Kim
Keyword(s):  
Phanerochaete Chrysosporium ◽  
De Novo ◽  
Gene Annotation ◽  
Draft Genome ◽  
Whole Genome ◽  
Content Type ◽  
Protein Encoding ◽  
Crucial Information ◽  
And Function ◽  
Encoding Genes

ABSTRACT Phanerochaete chrysosporium (ATCC 20696) has a catabolic ability to degrade lignin. Here, we report whole-genome sequencing used to identify genes related to lignin modification. We determined the 39-Mb draft genome sequence of this fungus, comprising 13,560 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes.

scholarly journals Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Fahad Al-Qurainy ◽  
Aref Alshameri ◽  
Abdel-Rhman Gaafar ◽  
Salim Khan ◽  
Mohammad Nadeem ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Average Frequency ◽  
Cyamopsis Tetragonoloba ◽  
Metabolic Pathway Analysis ◽  
Illumina Hiseq ◽  
Forage Crop ◽  
Kegg Pathways ◽  
Advanced Analysis

The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.

scholarly journals Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yvan Butera ◽  
Enatha Mukantwari ◽  
Maria Artesi ◽  
Jeanne d’arc Umuringa ◽  
Áine Niamh O’Toole ◽  
...  
Keyword(s):  
Genomic Sequencing ◽  
Whole Genome ◽  
Genome Sequences ◽  
Durable Response ◽  
Travel History ◽  
Transmission Rates ◽  
Spatio Temporal ◽  
Local Transmission ◽  
Lineage Diversity

AbstractCOVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.

scholarly journals Whole-Genome Sequencing and De Novo Assembly of 61 Staphylococcus pseudintermedius Isolates from Healthy Dogs and Dogs with Pyoderma

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
O. Francino ◽  
D. Pérez ◽  
J. Viñes ◽  
R. Fonticoba ◽  
S. Madroñero ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
De Novo ◽  
Noncoding Rnas ◽  
Whole Genome ◽  
Genome Sequences ◽  
Staphylococcus Pseudintermedius ◽  
Coding Sequences ◽  
Content Type ◽  
Long Reads ◽  
Healthy Dogs

ABSTRACT We have de novo assembled and polished 61 Staphylococcus pseudintermedius genome sequences with Nanopore-only long reads. Completeness was 99.25%. The average genome size was 2.70 Mbp, comprising 2,506 coding sequences, 19 complete rRNAs, 56 to 59 tRNAs, and 4 noncoding RNAs (ncRNAs), as well as CRISPR arrays.

scholarly journals The complete genome sequences of two species of seventeen-year cicadas: Magicicada septendecim and Magicicada septendecula

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 215
Author(s):  
Harold B. White ◽  
Stacy Pirro
Keyword(s):  
North America ◽  
Related Species ◽  
De Novo ◽  
Eastern North America ◽  
Whole Genome ◽  
Genome Sequences ◽  
Short Read ◽  
Short Read Archive ◽  
Periodical Cicadas ◽  
Ncbi Short Read Archive

The genus Magicicada (Hemiptera: Cicadidae) includes the periodical cicadas of Eastern North America. Spending the majority of their long lives underground, the adult cicadas emerge every 13 or 17 years to spend 4-6 weeks as adult to mate. We present the whole genome sequences of two species of 17-year cicadas, Magicicada septendecim and Magicicada septendecula. The reads were assembled by a de novo method followed by alignments to related species. Annotation was performed by GeneMark-ES. The raw and assembled data is available via NCBI Short Read Archive and Assembly databases.

scholarly journals De Novo Whole-Genome Sequencing and Annotation of Pathogenic Bovine Pasteurella multocida Type A:3 Strains

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
Morag Livingstone ◽  
Kevin Aitchison ◽  
Mark Dagleish ◽  
David Longbottom
Keyword(s):  
Genome Sequencing ◽  
Pasteurella Multocida ◽  
De Novo ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Pneumonic Pasteurellosis ◽  
The United Kingdom ◽  
The World ◽  
Welfare Implications

ABSTRACT Pneumonic pasteurellosis, caused by Pasteurella multocida, is a common respiratory infection of ruminants that has major economic and welfare implications throughout the world. Here, we report the annotated genome sequences of seven pathogenic strains of P. multocida that were isolated from cattle in the United Kingdom.

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