Database resources of the national center for biotechnology information

Sayers, Eric W; Bolton, Evan; Brister, J. Rodney; Canese, Kathi; Chan, Jessica; Comeau, Donald C.; Connor, Ryan; Funk, Kathryn; Kelly, Chris; Kim, Sunghwan; Madej, Tom; Marchler‐Bauer, Aron; Lanczycki, Christopher J.; Lathrop, Stacy; Lu, Zhiyong; Thibaud‐Nissen, Françoise; Murphy, Terence; Phan, Lon; Skripchenko, Yuri; Tse, Tony; Wang, Jiyao; Williams, Rebecca; Trawick, Barton W.; Pruitt, Kim D.; Sherry, Stephen T.

doi:10.1093/nar/gkab1112

Cited by 1,113 publications

(885 citation statements)

References 27 publications

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“…The 20-nt GmPDS8 guide sequence was used as query for nucleotide BLAST provided by National Center for Biotechnology Information (NCBI) [ 55 , 56 ] to search for similar sequences in the soybean genome. The non-PDS loci with top alignment scores were identified as potential off-targets.…”

Section: Methodsmentioning

confidence: 99%

An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

Lü

Tian

2022

BMC Biotechnol

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Background Genome editing by CRISPR/Cas9 has become a popular approach to induce targeted mutations for crop trait improvement. Soybean (Glycine max L. Merr.) is an economically important crop worldwide. Although gene editing has been demonstrated in soybean, its utilization in stably transformed plants through whole plant regeneration is still not widespread, largely due to difficulties with transformation or low mutation efficiencies. Results We sought to establish a simple, efficient, and specific CRISPR/Cas9 system to induce heritable mutations in soybean through stable transformation. We targeted phytoene desaturase (PDS) genes due to the distinctive dwarf and albino phenotypes of the loss of function mutant. To evaluate gene editing efficiency and specificity, three constructs targeting each of the two homologous soybean PDS genes specifically, as well as two constructs targeting both simultaneously with one guide RNA were created. Instead of using cotyledonary nodes from germinated seedlings, we used ‘half-seed’ explants derived from imbibed seeds for Agrobacterium-mediated transformation of cultivar Williams 82. Transformed plants for all five constructs were recovered. Dwarf and albino phenotypes were observed in transgenic plants harboring the constructs targeting both PDS genes. Gene editing at the desired loci was detected in the majority of T0 transgenic plants, with 75–100% mutation efficiencies. Indel frequencies varied widely among plants (3–100%), with those exhibiting visible mutant phenotypes showing higher frequencies (27–100%). Deletion was the predominant mutation type, although 1-nucleotide insertion was also observed. Constructs designed to target only one PDS gene did not induce mutation in the other homologous counterpart; and no mutation at several potential off-target loci was detected, indicating high editing specificity. Modifications in both PDS genes were transmitted to T1 progenies, including plants that were negative for transgene detection. Strong mutant phenotypes were also observed in T1 plants. Conclusions Using simple constructs containing one guide RNA, we demonstrated efficient and specific CRISPR/Cas9-mediated mutagenesis in stably transformed soybean plants, and showed that the mutations could be inherited in progenies, even in plants that lost transgenes through segregation. The established system can be employed to edit other genes for soybean trait improvement.

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Section: Methodsmentioning

confidence: 99%

An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

Lü

Tian

2022

BMC Biotechnol

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“…We downloaded existing Trichoptera genomes from GenBank [ 62 ] or Lepbase [ 58 ] and used these in conjunction with our newly generated genomes to analyze genome size evolution as explained in the following sections of this manuscript.…”

Section: Data Descriptionmentioning

confidence: 99%

Genome size evolution in the diverse insect order Trichoptera

et al. 2022

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Background Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities.

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“…Taxonomy was performed through the construction of a phylogenetic tree based on the alignment of partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) genes. Homologous sequences were identified using BlastN against the nr NCBI database [20]. The accession number of used genes is shown in Supplementary Table S1.…”

Section: Phylogenetic Relationships and Comparative Genomic Analysismentioning

confidence: 99%

“…Thus, the three domains are used in screening for PKSs. Then, the Pfam database [26] and NCBI CDD database [20] were used to scan for significant domains of these proteins. The conserved functional domains present in PKSs were further confirmed using Synthaser (v1.1.0) [27], and the function of these genes was predicted using NCBI BLASTP with an E-value of <1 × 10 −10 after setting up the online BLAST database [20].…”

Section: Identification Of Polyketide Synthase Genesmentioning

confidence: 99%

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Genome Mining and Analysis of PKS Genes in Eurotium cristatum E1 Isolated from Fuzhuan Brick Tea

Guo

Chen

Liu

et al. 2022

JoF

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Eurotium cristatum as the dominant fungi species of Fuzhuan brick tea in China, can produce multitudinous secondary metabolites (SMs) with various bioactivities. Polyketides are a very important class of SMs found in E. cristatum and have gained extensive attention in recent years due to their remarkable diversity of structures and multiple functions. Therefore, it is necessary to explore the polyketides produced by E. cristatum at the genomic level to enhance its application value. In this paper, 12 polyketide synthase (PKS) genes were found in the whole genome of E. cristatum E1 isolated from Fuzhuan brick tea. In addition, the qRT-PCR results further demonstrated that these genes were expressed. Moreover, metabolic analysis demonstrated E. cristatum E1 can produce a variety of polyketides, including citreorosein, emodin, physcion, isoaspergin, dihydroauroglaucin, iso-dihydroauroglaucin, aspergin, flavoglaucin and auroglaucin. Furthermore, based on genomic analysis, the putative secondary metabolites clusters for emodin and flavoglaucin were proposed. The results reported here will lay a good basis for systematically mining SMs resources of E. cristatum and broadening its application fields.

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Database resources of the national center for biotechnology information

Cited by 1,113 publications

References 27 publications

An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

An efficient and specific CRISPR-Cas9 genome editing system targeting soybean phytoene desaturase genes

Genome size evolution in the diverse insect order Trichoptera

Genome Mining and Analysis of PKS Genes in Eurotium cristatum E1 Isolated from Fuzhuan Brick Tea

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