scholarly journals Mikan Genome Database (MiGD): integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding

2020 ◽  
Vol 70 (2) ◽  
pp. 200-211 ◽  
Author(s):  
Yoshihiro Kawahara ◽  
Tomoko Endo ◽  
Mitsuo Omura ◽  
Yumiko Teramoto ◽  
Takeshi Itoh ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Molecular Breeding ◽  
Genomic Diversity ◽  
Caps Marker ◽  
Genome Database ◽  
Marker Information

scholarly journals Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hui Li ◽  
Xingyu Yang ◽  
Yue Zhang ◽  
Zhiyan Gao ◽  
Yuting Liang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Aquatic Plant ◽  
Molecular Breeding ◽  
Nelumbo Nucifera ◽  
Sequence Analyses ◽  
Genome Database ◽  
Future Studies ◽  
Sacred Lotus ◽  
Coexpression Networks

AbstractSacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus.

scholarly journals Bovine Genome Database: integrated tools for genome annotation and discovery

2010 ◽  
Vol 39 (suppl_1) ◽  
pp. D830-D834 ◽  
Author(s):  
Christopher P. Childers ◽  
Justin T. Reese ◽  
Jaideep P. Sundaram ◽  
Donald C. Vile ◽  
C. Michael Dickens ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Bovine Genome ◽  
Genome Database

scholarly journals Bovine Genome Database: new annotation tools for a new reference genome

2019 ◽  
Author(s):  
Md Shamimuzzaman ◽  
Justin J Le Tourneau ◽  
Deepak R Unni ◽  
Colin M Diesh ◽  
Deborah A Triant ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genome Annotation ◽  
Reference Genome ◽  
Gene Annotation ◽  
Bovine Genome ◽  
Data Retrieval ◽  
Genome Database ◽  
Ruminant Species ◽  
Search Tool ◽  
Efficient Data

Abstract The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.

scholarly journals Resequencing 250 soybean accessions: new insights into genes associated with agronomic traits and genetic networks

2021 ◽  
Author(s):  
Chunming Yang ◽  
Jun Yan ◽  
Shuqin Jiang ◽  
Xia Li ◽  
Haowei Min ◽  
...  
Keyword(s):  
Gene Network ◽  
Molecular Breeding ◽  
Selective Sweep ◽  
Agronomic Traits ◽  
Genetic Network ◽  
Genomic Diversity ◽  
Yield Traits ◽  
Isoflavone Content ◽  
Gene Network Analysis ◽  
Variety Traits

AbstractLimited knowledge on genomic diversity and the functional genes associated with soybean variety traits has resulted in slow breeding progress. We sequenced the genome of 250 soybean landraces and cultivars from China, America and Europe, and investigated their population structure, genetic diversity and architecture and selective sweep regions of accessions. We identified five novel agronomically important genes and studied the effects of functional mutations in respective genes. We found candidate genes GSTT1, GL3 and GSTL3 associated with isoflavone content, CKX3 associated with yield traits, and CYP85A2 associated with both architecture and yield traits. Our phenotype-gene network analysis revealed that hub nodes play a role in complex phenotypic associations. In this work, we describe novel agronomic trait associated genes and a complex genetic network, providing a valuable resource for future soybean molecular breeding.

scholarly journals Genomic profiling ofNitrospiraspecies reveals ecological success of comammoxNitrospira

2019 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Barth F. Smets
Keyword(s):  
Large Scale ◽  
Wastewater Treatment Plants ◽  
Phylogenetic Signal ◽  
Environmental Filtering ◽  
Genomic Diversity ◽  
Metagenomic Data ◽  
Hydroxylamine Oxidoreductase ◽  
Environmental Distribution ◽  
Genome Database ◽  
Ecological Success

AbstractNitrification was long thought to consist in the stepwise oxidation of ammonia to nitrite and of nitrite to nitrate by ammonia oxidizing and nitrite oxidizing microorganisms, respectively. Recently, single microorganisms capable of complete ammonia to nitrate oxidation (comammox) were identified in theNitrospiragenus. This genus, previously considered to only contain canonical nitrite oxidizers is diverse and has a broad environmental distribution. Yet, a global insight into the abundance, niche preference, and genomic diversity ofNitrospirais missing. Here, we established the largestNitrospiragenome database to date, revealing 68 putative species, most without cultivated representatives. We performed a global survey through read recruitment of metagenomic data from various environments against this database that identified that environmental filtering structures species distribution, without large scale biogeographical signal. The ecological success of comammoxNitrospirais evident as they outnumber and are more diverse than canonicalNitrospirain communities from all environments but wastewater treatment plants. We detect a phylogenetic signal inNitrospiraspecies habitat preference, that is strongest for canonicalNitrospiraspecies. ComammoxNitrospiraeco-evolutionary history is more complex with subclades achieving rapid niche divergence via horizontal transfer of genes, including that encoding the hydroxylamine oxidoreductase, one of the key enzymes involved in nitrification.

Molecular breeding of fragrant early-season hybrid rice using the BADH2 gene

2019 ◽  
Vol 51 (6) ◽  
Author(s):  
Zhonghua Sheng ◽  
Sajid Fiaz ◽  
Qianlong Li ◽  
Wei Chen ◽  
Xiangjin Wei ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Hybrid Rice ◽  
Early Season ◽  
Badh2 Gene
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